HEADER HYDROLASE 03-NOV-23 8X04 TITLE X-RAY CRYSTAL STRUCTURE OF GLYCOSIDE HYDROLASE FAMILY 6 TITLE 2 CELLOBIOHYDROLASE FROM PHANEROCHAETE CHRYSOSPORIUM PCCEL6A TITLE 3 C240S/C393S/D394A COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCANASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHANERODONTIA CHRYSOSPORIUM; SOURCE 3 ORGANISM_TAXID: 2822231; SOURCE 4 STRAIN: K-3; SOURCE 5 GENE: CEL6A; SOURCE 6 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: KM71H; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPICZALPHA KEYWDS GLYCOSIDE HYDROLASE FAMILY 6, CELLOBIOHYDROLASE, CELLULASE, CATALYTIC KEYWDS 2 DOMAIN, MUTANT, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.YAMAGUCHI,N.SUNAGAWA,M.TACHIOKA,K.IGARASHI REVDAT 1 20-NOV-24 8X04 0 JRNL AUTH S.YAMAGUCHI,N.SUNAGAWA,M.TACHIOKA,K.IGARASHI JRNL TITL ACTIVITY AND X-RAY CRYSTAL STRUCTURE OF CANDIDATE BASE JRNL TITL 2 CATALYST MUTANTS OF GLYCOSIDE HYDROLASE FAMILY 6 JRNL TITL 3 CELLOBIOHYDROLASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 190896 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.050 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.3900 - 2.3400 1.00 14301 151 0.1583 0.1818 REMARK 3 2 2.3400 - 1.8600 1.00 13890 147 0.1668 0.1769 REMARK 3 3 1.8600 - 1.6200 1.00 13838 147 0.1615 0.1903 REMARK 3 4 1.6200 - 1.4700 1.00 13736 145 0.1528 0.1746 REMARK 3 5 1.4700 - 1.3700 1.00 13687 146 0.1563 0.1693 REMARK 3 6 1.3700 - 1.2900 1.00 13685 144 0.1592 0.1835 REMARK 3 7 1.2900 - 1.2200 0.99 13567 144 0.1525 0.1633 REMARK 3 8 1.2200 - 1.1700 0.99 13538 144 0.1545 0.1466 REMARK 3 9 1.1700 - 1.1200 0.99 13473 142 0.1523 0.1648 REMARK 3 10 1.1200 - 1.0900 0.98 13334 142 0.1569 0.1532 REMARK 3 11 1.0900 - 1.0500 0.97 13181 139 0.1647 0.1621 REMARK 3 12 1.0500 - 1.0200 0.96 13098 138 0.1821 0.1791 REMARK 3 13 1.0200 - 0.9900 0.95 12881 137 0.1950 0.1996 REMARK 3 14 0.9900 - 0.9700 0.93 12687 134 0.2183 0.2508 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.076 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.299 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 3911 REMARK 3 ANGLE : 0.886 5421 REMARK 3 CHIRALITY : 0.083 603 REMARK 3 PLANARITY : 0.007 734 REMARK 3 DIHEDRAL : 5.738 568 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8X04 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1300042375. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-23 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 190992 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.970 REMARK 200 RESOLUTION RANGE LOW (A) : 46.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.1000 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) : 0.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : 8.30 REMARK 200 R MERGE FOR SHELL (I) : 0.64800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACETATE, SODIUM REMARK 280 CHLORIDE, PH 4.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 27.40650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.12900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.91250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.12900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.40650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.91250 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: MONOMERIC 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 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 TYR A 164 69.48 -151.65 REMARK 500 ASP A 165 32.51 -149.13 REMARK 500 ASN A 184 65.12 -119.84 REMARK 500 GLU A 214 74.25 52.21 REMARK 500 ASP A 216 -24.60 83.07 REMARK 500 SER A 217 -82.45 -121.51 REMARK 500 SER A 217 -82.45 -64.19 REMARK 500 TRP A 264 -71.88 -111.51 REMARK 500 ASN A 300 -164.68 -112.61 REMARK 500 TRP A 360 -21.70 -152.87 REMARK 500 SER A 406 0.28 -63.75 REMARK 500 ASP A 412 6.14 -68.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8WXC RELATED DB: PDB REMARK 900 RELATED ID: 8WY2 RELATED DB: PDB REMARK 900 RELATED ID: 8WYV RELATED DB: PDB REMARK 900 RELATED ID: 8X00 RELATED DB: PDB DBREF 8X04 A 82 439 UNP H3K419 H3K419_PHACH 82 439 SEQADV 8X04 SER A 240 UNP H3K419 CYS 240 ENGINEERED MUTATION SEQADV 8X04 SER A 393 UNP H3K419 CYS 393 ENGINEERED MUTATION SEQADV 8X04 ALA A 394 UNP H3K419 ASP 394 ENGINEERED MUTATION SEQRES 1 A 358 SER ALA ASN ASN PRO TRP THR GLY PHE GLN ILE PHE LEU SEQRES 2 A 358 SER PRO TYR TYR ALA ASN GLU VAL ALA ALA ALA ALA LYS SEQRES 3 A 358 GLN ILE THR ASP PRO THR LEU SER SER LYS ALA ALA SER SEQRES 4 A 358 VAL ALA ASN ILE PRO THR PHE THR TRP LEU ASP SER VAL SEQRES 5 A 358 ALA LYS ILE PRO ASP LEU GLY THR TYR LEU ALA SER ALA SEQRES 6 A 358 SER ALA LEU GLY LYS SER THR GLY THR LYS GLN LEU VAL SEQRES 7 A 358 GLN ILE VAL ILE TYR ASP LEU PRO ASP ARG ASP CYS ALA SEQRES 8 A 358 ALA LYS ALA SER ASN GLY GLU PHE SER ILE ALA ASN ASN SEQRES 9 A 358 GLY GLN ALA ASN TYR GLU ASN TYR ILE ASP GLN ILE VAL SEQRES 10 A 358 ALA GLN ILE GLN GLN PHE PRO ASP VAL ARG VAL VAL ALA SEQRES 11 A 358 VAL ILE GLU PRO ASP SER LEU ALA ASN LEU VAL THR ASN SEQRES 12 A 358 LEU ASN VAL GLN LYS CYS ALA ASN ALA LYS THR THR TYR SEQRES 13 A 358 LEU ALA SER VAL ASN TYR ALA LEU THR ASN LEU ALA LYS SEQRES 14 A 358 VAL GLY VAL TYR MET TYR MET ASP ALA GLY HIS ALA GLY SEQRES 15 A 358 TRP LEU GLY TRP PRO ALA ASN LEU SER PRO ALA ALA GLN SEQRES 16 A 358 LEU PHE THR GLN VAL TRP GLN ASN ALA GLY LYS SER PRO SEQRES 17 A 358 PHE ILE LYS GLY LEU ALA THR ASN VAL ALA ASN TYR ASN SEQRES 18 A 358 ALA LEU GLN ALA ALA SER PRO ASP PRO ILE THR GLN GLY SEQRES 19 A 358 ASN PRO ASN TYR ASP GLU ILE HIS TYR ILE ASN ALA LEU SEQRES 20 A 358 ALA PRO LEU LEU GLN GLN ALA GLY TRP ASP ALA THR PHE SEQRES 21 A 358 ILE VAL ASP GLN GLY ARG SER GLY VAL GLN ASN ILE ARG SEQRES 22 A 358 GLN GLN TRP GLY ASP TRP CYS ASN ILE LYS GLY ALA GLY SEQRES 23 A 358 PHE GLY THR ARG PRO THR THR ASN THR GLY SER GLN PHE SEQRES 24 A 358 ILE ASP SER ILE VAL TRP VAL LYS PRO GLY GLY GLU SER SEQRES 25 A 358 ALA GLY THR SER ASN SER SER SER PRO ARG TYR ASP SER SEQRES 26 A 358 THR CYS SER LEU PRO ASP ALA ALA GLN PRO ALA PRO GLU SEQRES 27 A 358 ALA GLY THR TRP PHE GLN ALA TYR PHE GLN THR LEU VAL SEQRES 28 A 358 SER ALA ALA ASN PRO PRO LEU HET NAG A 501 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG C8 H15 N O6 FORMUL 3 HOH *532(H2 O) HELIX 1 AA1 SER A 95 ILE A 109 1 15 HELIX 2 AA2 ASP A 111 VAL A 121 1 11 HELIX 3 AA3 ALA A 122 ILE A 124 5 3 HELIX 4 AA4 SER A 132 ALA A 134 5 3 HELIX 5 AA5 LYS A 135 GLY A 154 1 20 HELIX 6 AA6 ASN A 185 GLN A 202 1 18 HELIX 7 AA7 SER A 217 ASN A 224 1 8 HELIX 8 AA8 VAL A 227 LYS A 250 1 24 HELIX 9 AA9 TRP A 267 ALA A 285 1 19 HELIX 10 AB1 ASP A 310 GLN A 314 5 5 HELIX 11 AB2 ASP A 320 ALA A 335 1 16 HELIX 12 AB3 ASP A 405 LEU A 410 5 6 HELIX 13 AB4 PHE A 424 ALA A 434 1 11 SHEET 1 AA1 3 GLN A 91 ILE A 92 0 SHEET 2 AA1 3 GLN A 157 ILE A 163 1 O LEU A 158 N GLN A 91 SHEET 3 AA1 3 THR A 128 LEU A 130 1 N LEU A 130 O VAL A 162 SHEET 1 AA2 7 GLN A 91 ILE A 92 0 SHEET 2 AA2 7 GLN A 157 ILE A 163 1 O LEU A 158 N GLN A 91 SHEET 3 AA2 7 VAL A 207 ILE A 213 1 O VAL A 212 N ILE A 163 SHEET 4 AA2 7 TYR A 254 ASP A 258 1 O TYR A 254 N ALA A 211 SHEET 5 AA2 7 ILE A 291 THR A 296 1 O ALA A 295 N MET A 257 SHEET 6 AA2 7 THR A 340 ASP A 344 1 O ASP A 344 N THR A 296 SHEET 7 AA2 7 ILE A 381 VAL A 385 1 O VAL A 385 N VAL A 343 SSBOND 1 CYS A 171 CYS A 230 1555 1555 2.06 SSBOND 2 CYS A 361 CYS A 408 1555 1555 2.06 LINK ND2 ASN A 398 C1 NAG A 501 1555 1555 1.44 CISPEP 1 GLN A 415 PRO A 416 0 -3.44 CISPEP 2 GLN A 415 PRO A 416 0 0.34 CISPEP 3 ASN A 436 PRO A 437 0 1.00 CISPEP 4 ASN A 436 PRO A 437 0 6.43 CRYST1 54.813 67.825 88.258 90.00 90.00 90.00 P 21 21 21 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 0.018244 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014744 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011330 0.00000