HEADER HYDROLASE 20-APR-23 8OTA TITLE HIGH RESOLUTION CRYSTAL STRUCTURE OF A LEAF-BRANCH COMPOST CUTINASE TITLE 2 QUADRUPLE VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEAF-BRANCH COMPOST CUTINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LC-CUTINASE,LCC,PET-DIGESTING ENZYME,POLY(ETHYLENE COMPND 5 TEREPHTHALATE) HYDROLASE,PET HYDROLASE,PETASE; COMPND 6 EC: 3.1.1.74,3.1.1.101; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNCULTURED BACTERIUM; SOURCE 3 ORGANISM_TAXID: 77133; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HYDROLASE, SERINE ESTERASE, CUTINASE EXPDTA X-RAY DIFFRACTION AUTHOR S.GAVALDA,G.CIOCI,A.MARTY,S.DUQUESNE REVDAT 1 04-SEP-24 8OTA 0 JRNL AUTH C.CHARLIER,S.GAVALDA,J.GRGA,L.PERROT,V.GABRIELLI,F.LOHR, JRNL AUTH 2 J.SCHORGHUBER,R.LICHTENECKER,G.ARNAL,A.MARTY,V.TOURNIER, JRNL AUTH 3 G.LIPPENS JRNL TITL EXPLORING THE PH DEPENDENCE OF AN IMPROVED PETASE. JRNL REF BIOPHYS.J. V. 123 1542 2024 JRNL REFN ESSN 1542-0086 JRNL PMID 38664965 JRNL DOI 10.1016/J.BPJ.2024.04.026 REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 26667 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.280 REMARK 3 FREE R VALUE TEST SET COUNT : 1407 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 10.0000 - 3.7000 1.00 2602 180 0.1642 0.1828 REMARK 3 2 3.7000 - 2.9400 1.00 2557 124 0.1731 0.2078 REMARK 3 3 2.9400 - 2.5700 1.00 2526 138 0.1628 0.2001 REMARK 3 4 2.5700 - 2.3300 1.00 2512 153 0.1715 0.2073 REMARK 3 5 2.3300 - 2.1700 1.00 2519 139 0.1436 0.1832 REMARK 3 6 2.1700 - 2.0400 1.00 2523 124 0.1818 0.2097 REMARK 3 7 2.0400 - 1.9400 1.00 2498 132 0.1523 0.1656 REMARK 3 8 1.9400 - 1.8500 1.00 2503 132 0.1727 0.2234 REMARK 3 9 1.8500 - 1.7800 1.00 2490 136 0.2242 0.2547 REMARK 3 10 1.7800 - 1.7200 1.00 2530 149 0.3480 0.4270 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) : 0.245 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.444 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.22 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 : 0.007 2048 REMARK 3 ANGLE : 0.851 2815 REMARK 3 CHIRALITY : 0.060 319 REMARK 3 PLANARITY : 0.009 371 REMARK 3 DIHEDRAL : 5.897 306 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 8OTA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-APR-23. REMARK 100 THE DEPOSITION ID IS D_1292129987. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9677 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26667 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.719 REMARK 200 RESOLUTION RANGE LOW (A) : 36.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.63000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 (%): 45.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BICINE PH9, 10% PEG20000, 2% REMARK 280 DIOXANE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.79100 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 17.79100 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 17.79100 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 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 A 766 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 768 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 35 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 98 OG SER A 100 2.14 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 SER A 145 23.31 -142.96 REMARK 500 SER A 165 -126.70 64.35 REMARK 500 THR A 188 58.94 34.23 REMARK 500 HIS A 218 -82.94 -125.94 REMARK 500 ASN A 239 47.04 38.35 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 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 768 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A 769 DISTANCE = 6.41 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6THT RELATED DB: PDB REMARK 900 INACTIVE MUTANT DBREF 8OTA A 36 293 UNP G9BY57 PETH_UNKP 36 293 SEQADV 8OTA MET A 35 UNP G9BY57 INITIATING METHIONINE SEQADV 8OTA GLY A 127 UNP G9BY57 TYR 127 ENGINEERED MUTATION SEQADV 8OTA CYS A 238 UNP G9BY57 ASP 238 ENGINEERED MUTATION SEQADV 8OTA ILE A 243 UNP G9BY57 PHE 243 ENGINEERED MUTATION SEQADV 8OTA CYS A 283 UNP G9BY57 SER 283 ENGINEERED MUTATION SEQRES 1 A 259 MET SER ASN PRO TYR GLN ARG GLY PRO ASN PRO THR ARG SEQRES 2 A 259 SER ALA LEU THR ALA ASP GLY PRO PHE SER VAL ALA THR SEQRES 3 A 259 TYR THR VAL SER ARG LEU SER VAL SER GLY PHE GLY GLY SEQRES 4 A 259 GLY VAL ILE TYR TYR PRO THR GLY THR SER LEU THR PHE SEQRES 5 A 259 GLY GLY ILE ALA MET SER PRO GLY TYR THR ALA ASP ALA SEQRES 6 A 259 SER SER LEU ALA TRP LEU GLY ARG ARG LEU ALA SER HIS SEQRES 7 A 259 GLY PHE VAL VAL LEU VAL ILE ASN THR ASN SER ARG PHE SEQRES 8 A 259 ASP GLY PRO ASP SER ARG ALA SER GLN LEU SER ALA ALA SEQRES 9 A 259 LEU ASN TYR LEU ARG THR SER SER PRO SER ALA VAL ARG SEQRES 10 A 259 ALA ARG LEU ASP ALA ASN ARG LEU ALA VAL ALA GLY HIS SEQRES 11 A 259 SER MET GLY GLY GLY GLY THR LEU ARG ILE ALA GLU GLN SEQRES 12 A 259 ASN PRO SER LEU LYS ALA ALA VAL PRO LEU THR PRO TRP SEQRES 13 A 259 HIS THR ASP LYS THR PHE ASN THR SER VAL PRO VAL LEU SEQRES 14 A 259 ILE VAL GLY ALA GLU ALA ASP THR VAL ALA PRO VAL SER SEQRES 15 A 259 GLN HIS ALA ILE PRO PHE TYR GLN ASN LEU PRO SER THR SEQRES 16 A 259 THR PRO LYS VAL TYR VAL GLU LEU CYS ASN ALA SER HIS SEQRES 17 A 259 ILE ALA PRO ASN SER ASN ASN ALA ALA ILE SER VAL TYR SEQRES 18 A 259 THR ILE SER TRP MET LYS LEU TRP VAL ASP ASN ASP THR SEQRES 19 A 259 ARG TYR ARG GLN PHE LEU CYS ASN VAL ASN ASP PRO ALA SEQRES 20 A 259 LEU CYS ASP PHE ARG THR ASN ASN ARG HIS CYS GLN HET DIO A 301 6 HETNAM DIO 1,4-DIETHYLENE DIOXIDE FORMUL 2 DIO C4 H8 O2 FORMUL 3 HOH *369(H2 O) HELIX 1 AA1 THR A 46 ALA A 52 5 7 HELIX 2 AA2 SER A 64 VAL A 68 5 5 HELIX 3 AA3 ASP A 98 SER A 101 5 4 HELIX 4 AA4 LEU A 102 HIS A 112 1 11 HELIX 5 AA5 GLY A 127 SER A 145 1 19 HELIX 6 AA6 PRO A 147 ALA A 152 1 6 HELIX 7 AA7 SER A 165 ASN A 178 1 14 HELIX 8 AA8 HIS A 218 LEU A 226 1 9 HELIX 9 AA9 ILE A 243 SER A 247 5 5 HELIX 10 AB1 ASN A 249 ASP A 265 1 17 HELIX 11 AB2 ASP A 267 LEU A 274 5 8 HELIX 12 AB3 ASN A 289 GLN A 293 5 5 SHEET 1 AA1 6 SER A 57 VAL A 63 0 SHEET 2 AA1 6 GLY A 74 THR A 80 -1 O GLY A 74 N VAL A 63 SHEET 3 AA1 6 VAL A 115 ILE A 119 -1 O VAL A 116 N TYR A 77 SHEET 4 AA1 6 PHE A 86 SER A 92 1 N ILE A 89 O VAL A 115 SHEET 5 AA1 6 LEU A 154 HIS A 164 1 O ASP A 155 N PHE A 86 SHEET 6 AA1 6 ALA A 184 LEU A 187 1 O LEU A 187 N GLY A 163 SHEET 1 AA2 3 VAL A 202 ALA A 207 0 SHEET 2 AA2 3 LYS A 232 LEU A 237 1 O VAL A 235 N GLY A 206 SHEET 3 AA2 3 LEU A 282 THR A 287 -1 O ARG A 286 N TYR A 234 SSBOND 1 CYS A 238 CYS A 283 1555 1555 2.04 SSBOND 2 CYS A 275 CYS A 292 1555 1555 2.05 CRYST1 110.184 110.184 35.582 90.00 90.00 120.00 P 63 6 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 0.009076 0.005240 0.000000 0.00000 SCALE2 0.000000 0.010480 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028104 0.00000