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 2 29-NOV-23 7W69 1 REMARK 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