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HEADER HYDROLASE 01-DEC-21 7W69
TITLE CRYSTAL STRUCTURE OF A PSH1 MUTANT IN COMPLEX WITH EDO
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PSH1;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: UNIDENTIFIED;
SOURCE 3 ORGANISM_TAXID: 32644;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-28A
KEYWDS ALPHA/BETA DEHYDROGENASE, PLASTIC DEGRADATION, THERMO-STABLE,
KEYWDS 2 HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.GAO,P.LARA,Z.S.LI,X.HAN,R.WEI,W.D.LIU
REVDAT 1 14-SEP-22 7W69 0
JRNL AUTH L.PFAFF,J.GAO,Z.LI,A.JACKERING,G.WEBER,J.MICAN,Y.CHEN,
JRNL AUTH 2 W.DONG,X.HAN,C.G.FEILER,Y.F.AO,C.P.S.BADENHORST,D.BEDNAR,
JRNL AUTH 3 G.J.PALM,M.LAMMERS,J.DAMBORSKY,B.STRODEL,W.LIU,
JRNL AUTH 4 U.T.BORNSCHEUER,R.WEI
JRNL TITL MULTIPLE SUBSTRATE BINDING MODE-GUIDED ENGINEERING OF A
JRNL TITL 2 THERMOPHILIC PET HYDROLASE.
JRNL REF ACS CATALYSIS V. 12 9790 2022
JRNL REFN ESSN 2155-5435
JRNL PMID 35966606
JRNL DOI 10.1021/ACSCATAL.2C02275
REMARK 2
REMARK 2 RESOLUTION. 1.56 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.18.2_3874
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 : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.56
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.52
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 41965
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.165
REMARK 3 R VALUE (WORKING SET) : 0.164
REMARK 3 FREE R VALUE : 0.183
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010
REMARK 3 FREE R VALUE TEST SET COUNT : 2101
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 23.5200 - 3.3600 1.00 4092 209 0.1431 0.1444
REMARK 3 2 3.3600 - 2.6700 1.00 4010 213 0.1605 0.1687
REMARK 3 3 2.6700 - 2.3300 1.00 3982 219 0.1644 0.2074
REMARK 3 4 2.3300 - 2.1200 1.00 3967 200 0.1686 0.1966
REMARK 3 5 2.1200 - 1.9700 1.00 3962 215 0.1657 0.1906
REMARK 3 6 1.9700 - 1.8500 1.00 4019 195 0.1871 0.2255
REMARK 3 7 1.8500 - 1.7600 1.00 3951 217 0.1767 0.2219
REMARK 3 8 1.7600 - 1.6800 1.00 3975 207 0.1889 0.2315
REMARK 3 9 1.6800 - 1.6200 1.00 3960 216 0.1994 0.2225
REMARK 3 10 1.6200 - 1.5600 0.99 3946 210 0.2162 0.2245
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) : 0.130
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.010
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.33
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 : NULL NULL
REMARK 3 ANGLE : NULL NULL
REMARK 3 CHIRALITY : NULL NULL
REMARK 3 PLANARITY : NULL NULL
REMARK 3 DIHEDRAL : NULL NULL
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 7W69 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-DEC-21.
REMARK 100 THE DEPOSITION ID IS D_1300026059.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 19-FEB-21
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRF
REMARK 200 BEAMLINE : BL19U1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : GRAPHITE
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42273
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560
REMARK 200 RESOLUTION RANGE LOW (A) : 25.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 9.400
REMARK 200 R MERGE (I) : 0.11500
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 9.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1
REMARK 200 DATA REDUNDANCY IN SHELL : 6.40
REMARK 200 R MERGE FOR SHELL (I) : 0.60800
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: 7NEI
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 53.93
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG 4000, 0.1M NACIT, PH5.6, 9%
REMARK 280 ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
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 52.76300
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.67300
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.76300
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.67300
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 THR A 63 -0.77 67.93
REMARK 500 SER A 130 -119.32 58.26
REMARK 500 LEU A 175 32.60 -99.12
REMARK 500 HIS A 184 -93.39 -121.28
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 712 DISTANCE = 5.96 ANGSTROMS
REMARK 525 HOH A 713 DISTANCE = 6.01 ANGSTROMS
DBREF 7W69 A 1 258 PDB 7W69 7W69 1 258
SEQRES 1 A 258 GLU ASN PRO TYR GLU ARG GLY PRO ASP PRO THR GLU SER
SEQRES 2 A 258 SER ILE GLU ALA VAL ARG GLY PRO PHE ALA VAL ALA GLN
SEQRES 3 A 258 THR THR VAL SER ARG LEU GLN ALA ASP GLY PHE GLY GLY
SEQRES 4 A 258 GLY THR ILE TYR TYR PRO THR ASP THR SER GLN GLY THR
SEQRES 5 A 258 PHE GLY ALA VAL ALA ILE SER PRO GLY PHE THR ALA GLY
SEQRES 6 A 258 GLN GLU SER ILE ALA TRP LEU GLY PRO ARG ILE ALA SER
SEQRES 7 A 258 GLN GLY PHE VAL VAL ILE THR ILE ASP THR ILE THR ARG
SEQRES 8 A 258 LEU ASP GLN PRO ASP SER ARG GLY ARG GLN LEU GLN ALA
SEQRES 9 A 258 ALA LEU ASP HIS LEU ARG THR ASN SER VAL VAL ARG ASN
SEQRES 10 A 258 ARG ILE ASP PRO ASN ARG MET ALA VAL MET GLY HIS SER
SEQRES 11 A 258 MET GLY GLY GLY GLY ALA LEU SER ALA ALA ALA ASN ASN
SEQRES 12 A 258 THR SER LEU GLU ALA ALA ILE PRO LEU GLN GLY TRP HIS
SEQRES 13 A 258 THR ARG LYS ASN TRP SER SER VAL ARG THR PRO THR LEU
SEQRES 14 A 258 VAL VAL GLY ALA GLN LEU ASP THR ILE ALA PRO VAL SER
SEQRES 15 A 258 SER HIS SER GLU ALA PHE TYR ASN SER LEU PRO SER ASP
SEQRES 16 A 258 LEU ASP LYS ALA TYR MET GLU LEU ARG GLY ALA SER HIS
SEQRES 17 A 258 PHE VAL SER ASN THR PRO ASP THR THR THR ALA LYS TYR
SEQRES 18 A 258 SER ILE ALA TRP LEU LYS ARG PHE VAL ASP ASN ASP LEU
SEQRES 19 A 258 ARG TYR GLU GLN PHE LEU CYS PRO ALA PRO ASP ASP PHE
SEQRES 20 A 258 ALA ILE SER GLU TYR ARG ALA THR CYS PRO PHE
HET EDO A 301 10
HETNAM EDO 1,2-ETHANEDIOL
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 EDO C2 H6 O2
FORMUL 3 HOH *313(H2 O)
HELIX 1 AA1 THR A 11 ALA A 17 1 7
HELIX 2 AA2 GLY A 65 ALA A 70 5 6
HELIX 3 AA3 TRP A 71 SER A 78 1 8
HELIX 4 AA4 GLN A 94 LEU A 109 1 16
HELIX 5 AA5 SER A 130 ASN A 142 1 13
HELIX 6 AA6 HIS A 184 SER A 191 1 8
HELIX 7 AA7 SER A 207 THR A 213 5 7
HELIX 8 AA8 ASP A 215 ASP A 231 1 17
HELIX 9 AA9 ASP A 233 LEU A 240 5 8
SHEET 1 AA1 6 VAL A 24 VAL A 29 0
SHEET 2 AA1 6 GLY A 40 PRO A 45 -1 O GLY A 40 N VAL A 29
SHEET 3 AA1 6 PHE A 81 ILE A 86 -1 O VAL A 83 N TYR A 43
SHEET 4 AA1 6 PHE A 53 SER A 59 1 N VAL A 56 O ILE A 84
SHEET 5 AA1 6 ILE A 119 HIS A 129 1 O MET A 127 N ALA A 57
SHEET 6 AA1 6 ALA A 148 LEU A 152 1 O LEU A 152 N GLY A 128
SHEET 1 AA2 3 THR A 168 ALA A 173 0
SHEET 2 AA2 3 LYS A 198 LEU A 203 1 O ALA A 199 N VAL A 170
SHEET 3 AA2 3 ILE A 249 ALA A 254 -1 O GLU A 251 N GLU A 202
SSBOND 1 CYS A 241 CYS A 256 1555 1555 2.03
CISPEP 1 CYS A 241 PRO A 242 0 -1.68
CISPEP 2 CYS A 256 PRO A 257 0 -10.21
CRYST1 105.526 55.346 51.153 90.00 93.36 90.00 C 1 2 1 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 0.009476 0.000000 0.000557 0.00000
SCALE2 0.000000 0.018068 0.000000 0.00000
SCALE3 0.000000 0.000000 0.019583 0.00000
TER 1969 PHE A 258
MASTER 231 0 1 9 9 0 0 6 2285 1 12 20
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