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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
TER 1849 ILE A 265
MASTER 260 0 0 13 9 0 0 6 2052 1 4 22
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