HEADER TRANSFERASE 28-NOV-07 2VI8 TITLE CRYSTAL STRUCTURE OF S172ABSSHMT INTERNAL ALDIMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE HYDROXYMETHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-405; COMPND 5 EC: 2.1.2.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PRSETC KEYWDS SHMT, E53Q, FTHF, TRANSFERASE, ENZYME MEMORY, PYRIDOXAL KEYWDS 2 PHOSPHATE, ONE-CARBON METABOLISM, PLP-DEPENDENT ENZYMES EXPDTA X-RAY DIFFRACTION AUTHOR V.RAJARAM,B.S.BHAVANI,V.PRAKASH,N.APPAJI RAO,H.S.SAVITHRI, AUTHOR 2 M.R.N.MURTHY REVDAT 2 24-FEB-09 2VI8 1 VERSN REVDAT 1 18-DEC-07 2VI8 0 JRNL AUTH V.RAJARAM,B.S.BHAVANI,V.PRAKASH,N.APPAJI RAO, JRNL AUTH 2 H.S.SAVITHRI,M.R.N.MURTHY JRNL TITL CRYSTAL STRUCTURE OF S172ABSSHMT AND ITS COMPLEXES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 40319 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2140 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.67 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.71 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2844 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.4610 REMARK 3 BIN FREE R VALUE SET COUNT : 152 REMARK 3 BIN FREE R VALUE : 0.5640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3154 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 461 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.118 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.069 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.038 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3259 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4433 ; 1.104 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 420 ; 5.108 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 152 ;37.443 ;24.079 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 536 ;12.872 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;16.215 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 492 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2498 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1685 ; 0.190 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2268 ; 0.301 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 348 ; 0.098 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 90 ; 0.164 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 70 ; 0.102 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2080 ; 0.399 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3263 ; 0.678 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1304 ; 1.226 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1162 ; 1.959 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2VI8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-NOV-07. REMARK 100 THE PDBE ID CODE IS EBI-34447. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : OSMIC MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42463 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.66 REMARK 200 RESOLUTION RANGE LOW (A) : 30.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 5.5 REMARK 200 R MERGE (I) : 0.05 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.80 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.1 REMARK 200 R MERGE FOR SHELL (I) : 0.28 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIFFERENCE FOURIER METHODS REMARK 200 SOFTWARE USED: REFMAC5 REMARK 200 STARTING MODEL: PDB ENTRY 1KKJ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.1 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% MPD, 0.1M HEPES PH 7.5, 0.2 REMARK 280 MM EDTA, 5 MM 2-MERCAPTOETHANOL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 30.51650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.26000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.51650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.26000 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 GENERATING THE BIOMOLECULE 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 8810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.3 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, SER 172 TO ALA REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ALA A 170 CB 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 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 ALA A 52 44.15 -143.72 REMARK 500 ARG A 58 51.86 -141.37 REMARK 500 ALA A 170 154.28 121.47 REMARK 500 ALA A 173 57.05 -149.47 REMARK 500 LYS A 226 -135.60 89.20 REMARK 500 ASN A 310 -143.84 -131.85 REMARK 500 THR A 353 163.52 69.66 REMARK 500 ASN A 386 45.05 -140.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP A1406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A1407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A1408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A1409 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VGU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E53QBSSHMT WITH L- REMARK 900 SERINE REMARK 900 RELATED ID: 1YJY RELATED DB: PDB REMARK 900 K226M MUTANT OF SERINE HYDROXYMETHYLTRANSFERASE REMARK 900 FROM B.STEAROTHERMOPHILUS, COMPLEX WITH REMARK 900 SERINE REMARK 900 RELATED ID: 1YJS RELATED DB: PDB REMARK 900 K226Q MUTANT OF SERINE HYDROXYMETHYLTRANSFERASE REMARK 900 FROM B.STEAROTHERMOPHILUS, COMPLEX WITH REMARK 900 GLYCINE REMARK 900 RELATED ID: 1KL2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SERINE REMARK 900 HYDROXYMETHYLTRANSFERASECOMPLEXED WITH GLYCINE AND REMARK 900 5-FORMYL TETRAHYDROFOLATE REMARK 900 RELATED ID: 1KL1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SERINE REMARK 900 HYDROXYMETHYLTRANSFERASECOMPLEXED WITH GLYCINE REMARK 900 RELATED ID: 1KKP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SERINE REMARK 900 HYDROXYMETHYLTRANSFERASECOMPLEXED WITH SERINE REMARK 900 RELATED ID: 2VGS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E53QBSSHMT INTERNAL REMARK 900 ALDIMINE REMARK 900 RELATED ID: 1YJZ RELATED DB: PDB REMARK 900 K226M MUTANT OF SERINE HYDROXYMETHYLTRANSFERASE REMARK 900 FROM B.STEAROTHERMOPHILUS REMARK 900 RELATED ID: 2VGT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E53QBSSHMT WITH GLYCINE REMARK 900 RELATED ID: 2VGV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E53QBSSHMT OBTAINED IN REMARK 900 THE PRESENCE OF L-ALLO-THREONINE REMARK 900 RELATED ID: 1KKJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SERINE REMARK 900 HYDROXYMETHYLTRANSFERASE FROMB.STEAROTHERMOPHILUS REMARK 900 RELATED ID: 2VGW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E53QBSSHMT OBTAINED IN REMARK 900 THE PRESENCE OF GLYCINE AND 5-FOMYL REMARK 900 TETRAHYDROFOLATE REMARK 900 RELATED ID: 2VIB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF S172ABSSHMT OBTAINED IN REMARK 900 THE PRESENCE OF L-ALLO-THR REMARK 900 RELATED ID: 2VIA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF S172ABSSHMT L-SERINE REMARK 900 EXTERNAL ALDIMINE REMARK 900 RELATED ID: 2VI9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF S172ABSSHMT GLYCINE REMARK 900 EXTERNAL ALDIMINE DBREF 2VI8 A 1 405 UNP Q7SIB6 Q7SIB6_BACST 1 405 SEQADV 2VI8 ALA A 172 UNP Q7SIB6 SER 172 ENGINEERED MUTATION SEQRES 1 A 405 MET LYS TYR LEU PRO GLN GLN ASP PRO GLN VAL PHE ALA SEQRES 2 A 405 ALA ILE GLU GLN GLU ARG LYS ARG GLN HIS ALA LYS ILE SEQRES 3 A 405 GLU LEU ILE ALA SER GLU ASN PHE VAL SER ARG ALA VAL SEQRES 4 A 405 MET GLU ALA GLN GLY SER VAL LEU THR ASN LYS TYR ALA SEQRES 5 A 405 GLU GLY TYR PRO GLY ARG ARG TYR TYR GLY GLY CYS GLU SEQRES 6 A 405 TYR VAL ASP ILE VAL GLU GLU LEU ALA ARG GLU ARG ALA SEQRES 7 A 405 LYS GLN LEU PHE GLY ALA GLU HIS ALA ASN VAL GLN PRO SEQRES 8 A 405 HIS SER GLY ALA GLN ALA ASN MET ALA VAL TYR PHE THR SEQRES 9 A 405 VAL LEU GLU HIS GLY ASP THR VAL LEU GLY MET ASN LEU SEQRES 10 A 405 SER HIS GLY GLY HIS LEU THR HIS GLY SER PRO VAL ASN SEQRES 11 A 405 PHE SER GLY VAL GLN TYR ASN PHE VAL ALA TYR GLY VAL SEQRES 12 A 405 ASP PRO GLU THR HIS VAL ILE ASP TYR ASP ASP VAL ARG SEQRES 13 A 405 GLU LYS ALA ARG LEU HIS ARG PRO LYS LEU ILE VAL ALA SEQRES 14 A 405 ALA ALA ALA ALA TYR PRO ARG ILE ILE ASP PHE ALA LYS SEQRES 15 A 405 PHE ARG GLU ILE ALA ASP GLU VAL GLY ALA TYR LEU MET SEQRES 16 A 405 VAL ASP MET ALA HIS ILE ALA GLY LEU VAL ALA ALA GLY SEQRES 17 A 405 LEU HIS PRO ASN PRO VAL PRO TYR ALA HIS PHE VAL THR SEQRES 18 A 405 THR THR THR HIS LYS THR LEU ARG GLY PRO ARG GLY GLY SEQRES 19 A 405 MET ILE LEU CYS GLN GLU GLN PHE ALA LYS GLN ILE ASP SEQRES 20 A 405 LYS ALA ILE PHE PRO GLY ILE GLN GLY GLY PRO LEU MET SEQRES 21 A 405 HIS VAL ILE ALA ALA LYS ALA VAL ALA PHE GLY GLU ALA SEQRES 22 A 405 LEU GLN ASP ASP PHE LYS ALA TYR ALA LYS ARG VAL VAL SEQRES 23 A 405 ASP ASN ALA LYS ARG LEU ALA SER ALA LEU GLN ASN GLU SEQRES 24 A 405 GLY PHE THR LEU VAL SER GLY GLY THR ASP ASN HIS LEU SEQRES 25 A 405 LEU LEU VAL ASP LEU ARG PRO GLN GLN LEU THR GLY LYS SEQRES 26 A 405 THR ALA GLU LYS VAL LEU ASP GLU VAL GLY ILE THR VAL SEQRES 27 A 405 ASN LYS ASN THR ILE PRO TYR ASP PRO GLU SER PRO PHE SEQRES 28 A 405 VAL THR SER GLY ILE ARG ILE GLY THR ALA ALA VAL THR SEQRES 29 A 405 THR ARG GLY PHE GLY LEU GLU GLU MET ASP GLU ILE ALA SEQRES 30 A 405 ALA ILE ILE GLY LEU VAL LEU LYS ASN VAL GLY SER GLU SEQRES 31 A 405 GLN ALA LEU GLU GLU ALA ARG GLN ARG VAL ALA ALA LEU SEQRES 32 A 405 THR ASP HET PLP A1406 15 HET MPD A1407 8 HET MPD A1408 8 HET PO4 A1409 5 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM PO4 PHOSPHATE ION FORMUL 2 MPD 2(C6 H14 O2) FORMUL 3 PLP C8 H10 N O6 P FORMUL 4 PO4 O4 P 3- FORMUL 5 HOH *461(H2 O1) HELIX 1 1 TYR A 3 ASP A 8 1 6 HELIX 2 2 ASP A 8 LYS A 25 1 18 HELIX 3 3 SER A 36 GLY A 44 1 9 HELIX 4 4 SER A 45 LYS A 50 5 6 HELIX 5 5 CYS A 64 GLY A 83 1 20 HELIX 6 6 SER A 93 LEU A 106 1 14 HELIX 7 7 LEU A 117 GLY A 120 5 4 HELIX 8 8 ASN A 130 TYR A 136 1 7 HELIX 9 9 ASP A 151 ARG A 163 1 13 HELIX 10 10 ASP A 179 GLY A 191 1 13 HELIX 11 11 ILE A 201 ALA A 207 1 7 HELIX 12 12 GLN A 239 PHE A 251 1 13 HELIX 13 13 LEU A 259 GLN A 275 1 17 HELIX 14 14 GLN A 275 GLU A 299 1 25 HELIX 15 15 SER A 305 GLY A 307 5 3 HELIX 16 16 ARG A 318 GLN A 321 5 4 HELIX 17 17 THR A 323 VAL A 334 1 12 HELIX 18 18 THR A 360 ARG A 366 1 7 HELIX 19 19 GLY A 369 LYS A 385 1 17 HELIX 20 20 SER A 389 ASP A 405 1 17 SHEET 1 AA 2 ILE A 26 GLU A 27 0 SHEET 2 AA 2 ILE A 336 THR A 337 1 N THR A 337 O ILE A 26 SHEET 1 AB 2 GLY A 54 TYR A 55 0 SHEET 2 AB 2 ARG A 58 ARG A 59 -1 O ARG A 58 N TYR A 55 SHEET 1 AC 7 HIS A 86 ASN A 88 0 SHEET 2 AC 7 GLY A 234 CYS A 238 -1 O ILE A 236 N ASN A 88 SHEET 3 AC 7 PHE A 219 THR A 223 -1 O VAL A 220 N LEU A 237 SHEET 4 AC 7 TYR A 193 ASP A 197 1 O LEU A 194 N PHE A 219 SHEET 5 AC 7 LEU A 166 ALA A 169 1 O ILE A 167 N MET A 195 SHEET 6 AC 7 THR A 111 MET A 115 1 O LEU A 113 N VAL A 168 SHEET 7 AC 7 ASN A 137 TYR A 141 1 O ASN A 137 N VAL A 112 SHEET 1 AD 4 THR A 302 LEU A 303 0 SHEET 2 AD 4 LEU A 312 ASP A 316 -1 O ASP A 316 N THR A 302 SHEET 3 AD 4 GLY A 355 GLY A 359 -1 O ILE A 356 N VAL A 315 SHEET 4 AD 4 ASN A 339 ASN A 341 -1 O ASN A 339 N ARG A 357 LINK NZ LYS A 226 C4A PLP A1406 1555 1555 1.35 CISPEP 1 PHE A 251 PRO A 252 0 4.73 SITE 1 AC1 17 TYR A 51 SER A 93 GLY A 94 ALA A 95 SITE 2 AC1 17 HIS A 122 ASP A 197 ALA A 199 HIS A 200 SITE 3 AC1 17 THR A 223 HIS A 225 LYS A 226 GLY A 256 SITE 4 AC1 17 GLY A 257 HOH A2099 HOH A2186 HOH A2291 SITE 5 AC1 17 HOH A2304 SITE 1 AC2 10 TYR A 152 ARG A 156 GLU A 185 ILE A 186 SITE 2 AC2 10 GLN A 321 LEU A 322 HOH A2254 HOH A2257 SITE 3 AC2 10 HOH A2458 HOH A2459 SITE 1 AC3 4 PHE A 131 GLN A 135 TYR A 136 ILE A 254 SITE 1 AC4 5 GLU A 371 GLU A 375 HOH A2414 HOH A2460 SITE 2 AC4 5 HOH A2461 CRYST1 61.033 106.520 56.986 90.00 90.00 90.00 P 21 21 2 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 0.016385 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009388 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017548 0.00000