HEADER LYASE 03-AUG-25 9W68 TITLE CRYSTAL STRUCTURAL OF DSPETASE05 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PETASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.22.69; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTERIA LATREILLE ET AL. 1825; SOURCE 3 ORGANISM_TAXID: 629395; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI B; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 37762 KEYWDS POLYETHYLENE TEREPHTHALATE, PETASE, PLASTIC WASTE RECOVERY, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.WANG,B.XU REVDAT 1 08-JUL-26 9W68 0 JRNL AUTH L.ZHANG,X.ZHOU,Y.YUAN,H.LI,J.LI,Y.ZHOU,S.DU,Z.WANG,Y.HAN, JRNL AUTH 2 X.FAN,D.HAN,L.WANG,C.ZHU,S.YE,Y.WANG,B.XU JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF DSPETASE05 FOR JRNL TITL 2 THE DEGRADATION OF POLYETHYLENE TEREPHTHALATE. JRNL REF INT.J.BIOL.MACROMOL. V. 343 50252 2026 JRNL REFN ISSN 0141-8130 JRNL PMID 41548779 JRNL DOI 10.1016/J.IJBIOMAC.2026.150252 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 20003 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1009 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 25.3800 - 3.6900 1.00 2867 155 0.1912 0.1928 REMARK 3 2 3.6900 - 2.9300 1.00 2745 147 0.1845 0.2066 REMARK 3 3 2.9300 - 2.5600 1.00 2706 135 0.1860 0.2391 REMARK 3 4 2.5600 - 2.3300 1.00 2682 169 0.1813 0.1837 REMARK 3 5 2.3300 - 2.1600 1.00 2663 143 0.1753 0.2422 REMARK 3 6 2.1600 - 2.0300 1.00 2656 147 0.1673 0.2031 REMARK 3 7 2.0300 - 1.9300 0.99 2675 113 0.1751 0.2158 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) : 0.154 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.67 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 : 0.006 1896 REMARK 3 ANGLE : 0.764 2584 REMARK 3 CHIRALITY : 0.050 278 REMARK 3 PLANARITY : 0.006 344 REMARK 3 DIHEDRAL : 15.681 644 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 9W68 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 01-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1300062269. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20077 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 6LU7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES 42% PEG 200, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 25.37600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.78900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.60800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.78900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.37600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.60800 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 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 0 REMARK 465 THR A 1 REMARK 465 ASN A 2 REMARK 465 PRO A 3 REMARK 465 GLY A 4 REMARK 465 GLY A 5 REMARK 465 GLY A 6 REMARK 465 GLY A 7 REMARK 465 GLY A 8 REMARK 465 GLY A 9 REMARK 465 SER A 10 REMARK 465 ASN A 11 REMARK 465 PRO A 12 REMARK 465 ASP A 13 REMARK 465 THR A 14 REMARK 465 GLY A 15 REMARK 465 ASN A 266 REMARK 465 LEU A 267 REMARK 465 GLU A 268 REMARK 465 HIS A 269 REMARK 465 HIS A 270 REMARK 465 HIS A 271 REMARK 465 HIS A 272 REMARK 465 HIS A 273 REMARK 465 HIS A 274 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 LEU A 39 -43.26 73.24 REMARK 500 THR A 66 -1.44 67.11 REMARK 500 SER A 133 -123.22 65.49 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 502 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH A 503 DISTANCE = 6.88 ANGSTROMS REMARK 525 HOH A 504 DISTANCE = 7.29 ANGSTROMS DBREF 9W68 A 0 274 PDB 9W68 9W68 0 274 SEQRES 1 A 275 MET THR ASN PRO GLY GLY GLY GLY GLY GLY SER ASN PRO SEQRES 2 A 275 ASP THR GLY THR GLY PHE PRO GLY VAL SER SER PHE SER SEQRES 3 A 275 ALA ASP GLY SER PHE ALA THR THR SER GLY SER ALA GLY SEQRES 4 A 275 LEU SER CYS THR VAL PHE ARG PRO SER THR LEU GLY ALA SEQRES 5 A 275 ASN GLY LEU LYS HIS PRO ILE ILE VAL TRP GLY ASN GLY SEQRES 6 A 275 THR THR ALA SER PRO SER THR TYR SER GLY ILE LEU GLU SEQRES 7 A 275 HIS TRP ALA SER HIS GLY PHE VAL VAL ILE ALA ALA ASN SEQRES 8 A 275 THR SER ASN ALA GLY THR GLY GLN ASP MET LEU ASN CYS SEQRES 9 A 275 VAL ASP TYR LEU THR THR GLN ASN ASN ARG SER THR GLY SEQRES 10 A 275 THR TYR ALA ASN LYS LEU ASP LEU ASN ARG ILE GLY ALA SEQRES 11 A 275 ALA GLY HIS SER GLN GLY GLY GLY GLY THR ILE MET ALA SEQRES 12 A 275 GLY GLN ASP TYR ARG ILE LYS VAL THR ALA PRO PHE GLN SEQRES 13 A 275 PRO TYR THR ILE GLY LEU GLY HIS ASN SER SER SER GLN SEQRES 14 A 275 SER ASN GLN ASN GLY PRO MET PHE LEU MET THR GLY SER SEQRES 15 A 275 ALA ASP THR ILE ALA SER PRO THR LEU ASN ALA LEU PRO SEQRES 16 A 275 VAL TYR ASN ARG ALA ASN VAL PRO VAL PHE TRP GLY GLU SEQRES 17 A 275 LEU SER GLY ALA SER HIS PHE GLU PRO VAL GLY SER ALA SEQRES 18 A 275 GLY ASP PHE ARG GLY PRO SER THR ALA TRP PHE ARG TYR SEQRES 19 A 275 HIS LEU MET ASP ASP ALA SER ALA GLU ASP THR PHE TYR SEQRES 20 A 275 GLY SER ASN CYS ASP LEU CYS THR ASP ASN ASP TRP ASP SEQRES 21 A 275 VAL ARG ARG LYS GLY ILE ASN LEU GLU HIS HIS HIS HIS SEQRES 22 A 275 HIS HIS FORMUL 2 HOH *204(H2 O) HELIX 1 AA1 GLY A 50 LEU A 54 5 5 HELIX 2 AA2 SER A 68 THR A 71 5 4 HELIX 3 AA3 TYR A 72 HIS A 82 1 11 HELIX 4 AA4 GLY A 97 ARG A 113 1 17 HELIX 5 AA5 SER A 133 GLY A 143 1 11 HELIX 6 AA6 ASN A 164 GLN A 168 5 5 HELIX 7 AA7 SER A 187 ALA A 192 1 6 HELIX 8 AA8 ALA A 192 ALA A 199 1 8 HELIX 9 AA9 ALA A 220 ASP A 222 5 3 HELIX 10 AB1 PHE A 223 ASP A 237 1 15 HELIX 11 AB2 ASP A 238 SER A 240 5 3 HELIX 12 AB3 ALA A 241 TYR A 246 1 6 HELIX 13 AB4 CYS A 250 ASP A 255 1 6 SHEET 1 AA1 6 THR A 32 ALA A 37 0 SHEET 2 AA1 6 CYS A 41 PRO A 46 -1 O VAL A 43 N GLY A 35 SHEET 3 AA1 6 VAL A 85 ALA A 89 -1 O ALA A 88 N THR A 42 SHEET 4 AA1 6 HIS A 56 GLY A 62 1 N PRO A 57 O VAL A 85 SHEET 5 AA1 6 LEU A 122 HIS A 132 1 O GLY A 128 N VAL A 60 SHEET 6 AA1 6 VAL A 150 PHE A 154 1 O PHE A 154 N GLY A 131 SHEET 1 AA2 3 MET A 175 GLY A 180 0 SHEET 2 AA2 3 VAL A 203 LEU A 208 1 O LEU A 208 N THR A 179 SHEET 3 AA2 3 TRP A 258 LYS A 263 -1 O ARG A 261 N TRP A 205 SSBOND 1 CYS A 41 CYS A 103 1555 1555 2.13 SSBOND 2 CYS A 250 CYS A 253 1555 1555 2.04 CRYST1 50.752 71.216 71.578 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 0.019704 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014042 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013971 0.00000 CONECT 167 619 CONECT 619 167 CONECT 1723 1745 CONECT 1745 1723 MASTER 260 0 0 13 9 0 0 6 2052 1 4 22 END