HEADER TRANSFERASE 28-MAY-13 4KXV TITLE HUMAN TRANSKETOLASE IN COVALENT COMPLEX WITH DONOR KETOSE D-XYLULOSE- TITLE 2 5-PHOSPHATE, CRYSTAL 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSKETOLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TK; COMPND 5 EC: 2.2.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TKT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS THIAMIN DIPHOSPHATE, ENZYME CATALYSIS, PENTOSE PHOSPHATE PATHWAY, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.NEUMANN,S.LUEDTKE,R.FICNER,K.TITTMANN REVDAT 6 20-SEP-23 4KXV 1 REMARK REVDAT 5 04-AUG-21 4KXV 1 COMPND REMARK SEQADV HET REVDAT 5 2 1 HETNAM FORMUL LINK SITE REVDAT 5 3 1 ATOM REVDAT 4 04-SEP-19 4KXV 1 REMARK LINK REVDAT 3 15-NOV-17 4KXV 1 REMARK REVDAT 2 04-SEP-13 4KXV 1 JRNL REVDAT 1 21-AUG-13 4KXV 0 JRNL AUTH S.LUDTKE,P.NEUMANN,K.M.ERIXON,F.LEEPER,R.KLUGER,R.FICNER, JRNL AUTH 2 K.TITTMANN JRNL TITL SUB-ANGSTROM-RESOLUTION CRYSTALLOGRAPHY REVEALS PHYSICAL JRNL TITL 2 DISTORTIONS THAT ENHANCE REACTIVITY OF A COVALENT ENZYMATIC JRNL TITL 3 INTERMEDIATE. JRNL REF NAT CHEM V. 5 762 2013 JRNL REFN ISSN 1755-4330 JRNL PMID 23965678 JRNL DOI 10.1038/NCHEM.1728 REMARK 2 REMARK 2 RESOLUTION. 0.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.096 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.094 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.114 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 15885 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 301825 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.084 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.082 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.102 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 13625 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 258570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4747 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 957 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 56477 REMARK 3 NUMBER OF RESTRAINTS : 60863 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 320.0 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.000 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 5.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 8.000 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.124 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.017 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.000 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.132 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY ? REMARK 4 REMARK 4 4KXV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000079931. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93939 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 301825 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.970 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.36500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.550 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 3MOS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR MIXTURE OF 13.5-15 % PEG REMARK 280 6000 (W/V), 4% PEG 400 (V/V), 2 % GLYCEROL (V/V) , PH 7.9, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 279.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 56.83500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.99000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.83500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 42.99000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A7231 LIES ON A SPECIAL POSITION. REMARK 375 HOH A7332 LIES ON A SPECIAL POSITION. REMARK 375 HOH A7458 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 LYS A 622 REMARK 465 ALA A 623 REMARK 465 LEU A 624 REMARK 465 VAL A 625 REMARK 465 PRO A 626 REMARK 465 ARG A 627 REMARK 465 GLY A 628 REMARK 465 SER A 629 REMARK 465 LEU A 630 REMARK 465 GLU A 631 REMARK 465 HIS A 632 REMARK 465 HIS A 633 REMARK 465 HIS A 634 REMARK 465 HIS A 635 REMARK 465 HIS A 636 REMARK 465 HIS A 637 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 8 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 64 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ALA A 121 CA - C - N ANGL. DEV. = 15.3 DEGREES REMARK 500 ALA A 121 O - C - N ANGL. DEV. = -14.0 DEGREES REMARK 500 ALA A 121 O - C - N ANGL. DEV. = 13.9 DEGREES REMARK 500 THR A 122 CA - C - N ANGL. DEV. = 16.6 DEGREES REMARK 500 THR A 122 CA - C - N ANGL. DEV. = -21.0 DEGREES REMARK 500 THR A 122 O - C - N ANGL. DEV. = -20.1 DEGREES REMARK 500 THR A 122 O - C - N ANGL. DEV. = 10.4 DEGREES REMARK 500 GLY A 123 C - N - CA ANGL. DEV. = 20.9 DEGREES REMARK 500 ARG A 148 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP A 200 CB - CG - OD1 ANGL. DEV. = 9.1 DEGREES REMARK 500 VAL A 221 CB - CA - C ANGL. DEV. = 12.2 DEGREES REMARK 500 VAL A 221 N - CA - CB ANGL. DEV. = -16.0 DEGREES REMARK 500 VAL A 221 CA - CB - CG1 ANGL. DEV. = 13.1 DEGREES REMARK 500 GLN A 230 CB - CG - CD ANGL. DEV. = 16.8 DEGREES REMARK 500 LYS A 232 C - N - CA ANGL. DEV. = 16.1 DEGREES REMARK 500 LYS A 232 CA - C - O ANGL. DEV. = -25.3 DEGREES REMARK 500 LYS A 232 O - C - N ANGL. DEV. = 18.5 DEGREES REMARK 500 GLU A 273 OE1 - CD - OE2 ANGL. DEV. = -7.5 DEGREES REMARK 500 TYR A 275 CG - CD2 - CE2 ANGL. DEV. = 5.6 DEGREES REMARK 500 TYR A 275 CZ - CE2 - CD2 ANGL. DEV. = -8.2 DEGREES REMARK 500 SER A 332 N - CA - CB ANGL. DEV. = -13.8 DEGREES REMARK 500 ASP A 333 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 334 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 334 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 395 NE - CZ - NH1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 395 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 LEU A 412 CA - CB - CG ANGL. DEV. = 23.3 DEGREES REMARK 500 ARG A 474 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 474 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 530 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 555 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 617 CD - NE - CZ ANGL. DEV. = 9.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 54 -52.74 -140.93 REMARK 500 PHE A 142 -63.93 -104.99 REMARK 500 ARG A 186 -27.83 82.74 REMARK 500 GLN A 196 -127.34 49.50 REMARK 500 SER A 256 8.44 81.76 REMARK 500 TYR A 363 -169.22 65.74 REMARK 500 ALA A 365 70.20 -161.76 REMARK 500 PHE A 535 -64.27 73.77 REMARK 500 PHE A 535 -64.27 72.82 REMARK 500 PRO A 593 -160.66 -78.36 REMARK 500 PRO A 593 -153.27 -80.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 23 0.10 SIDE CHAIN REMARK 500 ARG A 101 0.09 SIDE CHAIN REMARK 500 ARG A 302 0.13 SIDE CHAIN REMARK 500 ARG A 358 0.10 SIDE CHAIN REMARK 500 ARG A 550 0.15 SIDE CHAIN REMARK 500 ARG A 617 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 DX5 A1011 IS A HYDROLYZED D-XYULOSE-5-PHOSPHATE COVALENTLY LINKED REMARK 600 TO TDP A1012 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 155 OD1 REMARK 620 2 ASN A 185 OD1 94.3 REMARK 620 3 LEU A 187 O 102.7 90.2 REMARK 620 4 TPP A1011 O2A 85.2 176.6 93.1 REMARK 620 5 TPP A1011 O1B 164.5 94.2 90.2 85.5 REMARK 620 6 HOH A7001 O 82.7 84.8 172.9 91.9 85.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1008 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1009 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1010 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TPP A 1011 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DX5 A 1012 DBREF 4KXV A 1 623 UNP P29401 TKT_HUMAN 1 623 SEQADV 4KXV LEU A 624 UNP P29401 EXPRESSION TAG SEQADV 4KXV VAL A 625 UNP P29401 EXPRESSION TAG SEQADV 4KXV PRO A 626 UNP P29401 EXPRESSION TAG SEQADV 4KXV ARG A 627 UNP P29401 EXPRESSION TAG SEQADV 4KXV GLY A 628 UNP P29401 EXPRESSION TAG SEQADV 4KXV SER A 629 UNP P29401 EXPRESSION TAG SEQADV 4KXV LEU A 630 UNP P29401 EXPRESSION TAG SEQADV 4KXV GLU A 631 UNP P29401 EXPRESSION TAG SEQADV 4KXV HIS A 632 UNP P29401 EXPRESSION TAG SEQADV 4KXV HIS A 633 UNP P29401 EXPRESSION TAG SEQADV 4KXV HIS A 634 UNP P29401 EXPRESSION TAG SEQADV 4KXV HIS A 635 UNP P29401 EXPRESSION TAG SEQADV 4KXV HIS A 636 UNP P29401 EXPRESSION TAG SEQADV 4KXV HIS A 637 UNP P29401 EXPRESSION TAG SEQRES 1 A 637 MET GLU SER TYR HIS LYS PRO ASP GLN GLN LYS LEU GLN SEQRES 2 A 637 ALA LEU LYS ASP THR ALA ASN ARG LEU ARG ILE SER SER SEQRES 3 A 637 ILE GLN ALA THR THR ALA ALA GLY SER GLY HIS PRO THR SEQRES 4 A 637 SER CYS CYS SER ALA ALA GLU ILE MET ALA VAL LEU PHE SEQRES 5 A 637 PHE HIS THR MET ARG TYR LYS SER GLN ASP PRO ARG ASN SEQRES 6 A 637 PRO HIS ASN ASP ARG PHE VAL LEU SER LYS GLY HIS ALA SEQRES 7 A 637 ALA PRO ILE LEU TYR ALA VAL TRP ALA GLU ALA GLY PHE SEQRES 8 A 637 LEU ALA GLU ALA GLU LEU LEU ASN LEU ARG LYS ILE SER SEQRES 9 A 637 SER ASP LEU ASP GLY HIS PRO VAL PRO LYS GLN ALA PHE SEQRES 10 A 637 THR ASP VAL ALA THR GLY SER LEU GLY GLN GLY LEU GLY SEQRES 11 A 637 ALA ALA CYS GLY MET ALA TYR THR GLY LYS TYR PHE ASP SEQRES 12 A 637 LYS ALA SER TYR ARG VAL TYR CYS LEU LEU GLY ASP GLY SEQRES 13 A 637 GLU LEU SER GLU GLY SER VAL TRP GLU ALA MET ALA PHE SEQRES 14 A 637 ALA SER ILE TYR LYS LEU ASP ASN LEU VAL ALA ILE LEU SEQRES 15 A 637 ASP ILE ASN ARG LEU GLY GLN SER ASP PRO ALA PRO LEU SEQRES 16 A 637 GLN HIS GLN MET ASP ILE TYR GLN LYS ARG CYS GLU ALA SEQRES 17 A 637 PHE GLY TRP HIS ALA ILE ILE VAL ASP GLY HIS SER VAL SEQRES 18 A 637 GLU GLU LEU CYS LYS ALA PHE GLY GLN ALA LYS HIS GLN SEQRES 19 A 637 PRO THR ALA ILE ILE ALA LYS THR PHE LYS GLY ARG GLY SEQRES 20 A 637 ILE THR GLY VAL GLU ASP LYS GLU SER TRP HIS GLY LYS SEQRES 21 A 637 PRO LEU PRO LYS ASN MET ALA GLU GLN ILE ILE GLN GLU SEQRES 22 A 637 ILE TYR SER GLN ILE GLN SER LYS LYS LYS ILE LEU ALA SEQRES 23 A 637 THR PRO PRO GLN GLU ASP ALA PRO SER VAL ASP ILE ALA SEQRES 24 A 637 ASN ILE ARG MET PRO SER LEU PRO SER TYR LYS VAL GLY SEQRES 25 A 637 ASP LYS ILE ALA THR ARG LYS ALA TYR GLY GLN ALA LEU SEQRES 26 A 637 ALA LYS LEU GLY HIS ALA SER ASP ARG ILE ILE ALA LEU SEQRES 27 A 637 ASP GLY ASP THR LYS ASN SER THR PHE SER GLU ILE PHE SEQRES 28 A 637 LYS LYS GLU HIS PRO ASP ARG PHE ILE GLU CYS TYR ILE SEQRES 29 A 637 ALA GLU GLN ASN MET VAL SER ILE ALA VAL GLY CYS ALA SEQRES 30 A 637 THR ARG ASN ARG THR VAL PRO PHE CYS SER THR PHE ALA SEQRES 31 A 637 ALA PHE PHE THR ARG ALA PHE ASP GLN ILE ARG MET ALA SEQRES 32 A 637 ALA ILE SER GLU SER ASN ILE ASN LEU CYS GLY SER HIS SEQRES 33 A 637 CYS GLY VAL SER ILE GLY GLU ASP GLY PRO SER GLN MET SEQRES 34 A 637 ALA LEU GLU ASP LEU ALA MET PHE ARG SER VAL PRO THR SEQRES 35 A 637 SER THR VAL PHE TYR PRO SER ASP GLY VAL ALA THR GLU SEQRES 36 A 637 LYS ALA VAL GLU LEU ALA ALA ASN THR LYS GLY ILE CYS SEQRES 37 A 637 PHE ILE ARG THR SER ARG PRO GLU ASN ALA ILE ILE TYR SEQRES 38 A 637 ASN ASN ASN GLU ASP PHE GLN VAL GLY GLN ALA LYS VAL SEQRES 39 A 637 VAL LEU LYS SER LYS ASP ASP GLN VAL THR VAL ILE GLY SEQRES 40 A 637 ALA GLY VAL THR LEU HIS GLU ALA LEU ALA ALA ALA GLU SEQRES 41 A 637 LEU LEU LYS LYS GLU LYS ILE ASN ILE ARG VAL LEU ASP SEQRES 42 A 637 PRO PHE THR ILE LYS PRO LEU ASP ARG LYS LEU ILE LEU SEQRES 43 A 637 ASP SER ALA ARG ALA THR LYS GLY ARG ILE LEU THR VAL SEQRES 44 A 637 GLU ASP HIS TYR TYR GLU GLY GLY ILE GLY GLU ALA VAL SEQRES 45 A 637 SER SER ALA VAL VAL GLY GLU PRO GLY ILE THR VAL THR SEQRES 46 A 637 HIS LEU ALA VAL ASN ARG VAL PRO ARG SER GLY LYS PRO SEQRES 47 A 637 ALA GLU LEU LEU LYS MET PHE GLY ILE ASP ARG ASP ALA SEQRES 48 A 637 ILE ALA GLN ALA VAL ARG GLY LEU ILE THR LYS ALA LEU SEQRES 49 A 637 VAL PRO ARG GLY SER LEU GLU HIS HIS HIS HIS HIS HIS HET CA A1001 1 HET EDO A1002 4 HET EDO A1003 4 HET EDO A1004 4 HET EDO A1005 8 HET EDO A1006 4 HET EDO A1007 4 HET EDO A1008 4 HET EDO A1009 4 HET EDO A1010 4 HET TPP A1011 26 HET DX5 A1012 24 HETNAM CA CALCIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM TPP THIAMINE DIPHOSPHATE HETNAM DX5 D-XYLITOL-5-PHOSPHATE HETSYN EDO ETHYLENE GLYCOL HETSYN DX5 D-HYLITOL-5-PHOSPHATE FORMUL 2 CA CA 2+ FORMUL 3 EDO 9(C2 H6 O2) FORMUL 12 TPP C12 H19 N4 O7 P2 S 1+ FORMUL 13 DX5 C5 H13 O8 P FORMUL 14 HOH *957(H2 O) HELIX 1 1 ASP A 8 GLY A 34 1 27 HELIX 2 2 HIS A 37 SER A 43 1 7 HELIX 3 3 ALA A 44 HIS A 54 1 11 HELIX 4 4 LYS A 75 HIS A 77 5 3 HELIX 5 5 ALA A 78 ALA A 89 1 12 HELIX 6 6 ALA A 93 LEU A 100 5 8 HELIX 7 7 GLN A 127 PHE A 142 1 16 HELIX 8 8 GLY A 156 SER A 159 5 4 HELIX 9 9 GLU A 160 TYR A 173 1 14 HELIX 10 10 GLN A 198 PHE A 209 1 12 HELIX 11 11 SER A 220 GLN A 230 1 11 HELIX 12 12 PRO A 263 SER A 276 1 14 HELIX 13 13 THR A 317 SER A 332 1 16 HELIX 14 14 THR A 342 PHE A 347 1 6 HELIX 15 15 SER A 348 HIS A 355 1 8 HELIX 16 16 ALA A 365 THR A 378 1 14 HELIX 17 17 ARG A 379 ARG A 381 5 3 HELIX 18 18 ALA A 391 ARG A 395 5 5 HELIX 19 19 ALA A 396 SER A 406 1 11 HELIX 20 20 GLY A 418 GLY A 422 5 5 HELIX 21 21 GLY A 425 MET A 429 5 5 HELIX 22 22 GLU A 432 SER A 439 1 8 HELIX 23 23 ASP A 450 ASN A 463 1 14 HELIX 24 24 GLY A 509 LYS A 524 1 16 HELIX 25 25 ASP A 541 THR A 552 1 12 HELIX 26 26 GLY A 567 VAL A 577 1 11 HELIX 27 27 LYS A 597 PHE A 605 1 9 HELIX 28 28 ASP A 608 THR A 621 1 14 SHEET 1 A 5 ARG A 70 LEU A 73 0 SHEET 2 A 5 VAL A 149 GLY A 154 1 O TYR A 150 N VAL A 72 SHEET 3 A 5 LEU A 178 ILE A 184 1 O ASP A 183 N LEU A 153 SHEET 4 A 5 THR A 236 LYS A 241 1 O ILE A 238 N LEU A 182 SHEET 5 A 5 HIS A 212 ASP A 217 1 N ILE A 214 O ILE A 239 SHEET 1 B 2 LYS A 314 ALA A 316 0 SHEET 2 B 2 GLU A 476 ALA A 478 -1 O ASN A 477 N ILE A 315 SHEET 1 C 7 PHE A 359 GLU A 361 0 SHEET 2 C 7 ILE A 335 ASP A 339 1 N ALA A 337 O ILE A 360 SHEET 3 C 7 VAL A 383 PHE A 389 1 O PHE A 385 N LEU A 338 SHEET 4 C 7 ILE A 410 SER A 415 1 O ASN A 411 N CYS A 386 SHEET 5 C 7 ILE A 467 ARG A 471 1 O CYS A 468 N LEU A 412 SHEET 6 C 7 SER A 443 PHE A 446 1 N PHE A 446 O PHE A 469 SHEET 7 C 7 THR A 536 LYS A 538 -1 O LYS A 538 N VAL A 445 SHEET 1 D 5 LYS A 493 LEU A 496 0 SHEET 2 D 5 ASN A 528 ASP A 533 -1 O ASP A 533 N LYS A 493 SHEET 3 D 5 ASP A 501 ILE A 506 1 N VAL A 505 O ARG A 530 SHEET 4 D 5 ARG A 555 TYR A 563 1 O LEU A 557 N ILE A 506 SHEET 5 D 5 THR A 583 VAL A 589 1 O LEU A 587 N THR A 558 LINK C2 TPP A1011 C2 ADX5 A1012 1555 1555 1.53 LINK OD1 ASP A 155 CA CA A1001 1555 1555 2.02 LINK OD1 ASN A 185 CA CA A1001 1555 1555 2.11 LINK O LEU A 187 CA CA A1001 1555 1555 2.06 LINK CA CA A1001 O2A TPP A1011 1555 1555 2.05 LINK CA CA A1001 O1B TPP A1011 1555 1555 2.07 LINK CA CA A1001 O HOH A7001 1555 1555 2.22 CISPEP 1 LYS A 538 PRO A 539 0 -2.27 SITE 1 AC1 5 ASP A 155 ASN A 185 LEU A 187 TPP A1011 SITE 2 AC1 5 HOH A7001 SITE 1 AC2 8 PRO A 63 ASN A 68 ASP A 69 ARG A 70 SITE 2 AC2 8 PHE A 71 ARG A 379 HOH A7185 HOH A7887 SITE 1 AC3 8 PHE A 71 VAL A 72 LEU A 73 LEU A 82 SITE 2 AC3 8 PHE A 117 HOH A7043 HOH A7059 HOH A7081 SITE 1 AC4 7 TYR A 564 ALA A 588 ASN A 590 HOH A7035 SITE 2 AC4 7 HOH A7051 HOH A7134 HOH A7250 SITE 1 AC5 10 ARG A 21 SER A 25 ALA A 84 ALA A 87 SITE 2 AC5 10 GLU A 88 GLU A 94 LEU A 97 LYS A 283 SITE 3 AC5 10 HOH A7317 HOH A7643 SITE 1 AC6 7 LEU A 92 ASP A 106 LEU A 107 GLN A 115 SITE 2 AC6 7 HOH A7117 HOH A7124 HOH A7162 SITE 1 AC7 6 GLN A 10 LYS A 11 ASN A 590 ARG A 591 SITE 2 AC7 6 HOH A7309 HOH A7885 SITE 1 AC8 10 ALA A 33 LEU A 100 ARG A 101 LYS A 102 SITE 2 AC8 10 GLU A 423 LYS A 597 HOH A7104 HOH A7916 SITE 3 AC8 10 HOH A7935 HOH A7948 SITE 1 AC9 8 LEU A 158 TRP A 164 LEU A 195 ARG A 205 SITE 2 AC9 8 HOH A7040 HOH A7149 HOH A7803 HOH A7866 SITE 1 BC1 6 TYR A 137 TYR A 141 TYR A 173 HOH A7364 SITE 2 BC1 6 HOH A7500 HOH A7728 SITE 1 BC2 26 SER A 40 LYS A 75 HIS A 77 GLY A 123 SITE 2 BC2 26 SER A 124 LEU A 125 GLY A 154 ASP A 155 SITE 3 BC2 26 GLY A 156 GLU A 157 GLU A 160 ASN A 185 SITE 4 BC2 26 LEU A 187 GLY A 188 GLN A 189 LYS A 244 SITE 5 BC2 26 HIS A 258 ASP A 341 ILE A 364 GLU A 366 SITE 6 BC2 26 PHE A 392 ARG A 395 GLN A 428 CA A1001 SITE 7 BC2 26 DX5 A1012 HOH A7001 SITE 1 BC3 21 HIS A 37 HIS A 77 HIS A 110 GLN A 189 SITE 2 BC3 21 HIS A 258 ARG A 318 SER A 345 PHE A 389 SITE 3 BC3 21 HIS A 416 ASP A 424 GLN A 428 ARG A 474 SITE 4 BC3 21 TPP A1011 HOH A7067 HOH A7102 HOH A7121 SITE 5 BC3 21 HOH A7273 HOH A7297 HOH A7427 HOH A7738 SITE 6 BC3 21 HOH A7957 CRYST1 113.670 85.980 73.000 90.00 125.30 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008797 0.000000 0.006229 0.00000 SCALE2 0.000000 0.011631 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016785 0.00000