HEADER ISOMERASE 11-FEB-15 5AI1 TITLE CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE CONTAINING Y32F, D40N, Y57F TITLE 2 AND Y119F MUTATIONS IN THE EQUILENIN-BOUND FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: KETOSTEROID ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 VARIANT: BIOTYPE B; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PKK223-3 KEYWDS ISOMERASE, KETOSTEROID ISOMERASE, PSEUDOMONAS PUTIDA, EQUILENIN EXPDTA X-RAY DIFFRACTION AUTHOR H.J.CHA,J.H.JEONG,Y.G.KIM REVDAT 5 10-JAN-24 5AI1 1 REMARK REVDAT 4 23-SEP-15 5AI1 1 REMARK REVDAT 3 17-JUN-15 5AI1 1 REMARK REVDAT 2 10-JUN-15 5AI1 1 JRNL REVDAT 1 20-MAY-15 5AI1 0 JRNL AUTH D.S.JANG,G.CHOI,H.J.CHA,S.SHIN,B.H.HONG,H.J.LEE,H.C.LEE, JRNL AUTH 2 K.Y.CHOI JRNL TITL CONTRIBUTION OF A LOW-BARRIER HYDROGEN BOND TO CATALYSIS IS JRNL TITL 2 NOT SIGNIFICANT IN KETOSTEROID ISOMERASE. JRNL REF MOL.CELLS V. 38 409 2015 JRNL REFN ISSN 1016-8478 JRNL PMID 25947291 JRNL DOI 10.14348/MOLCELLS.2015.2266 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 7121 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 712 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 30.1368 - 3.5944 0.99 1414 156 0.1538 0.2141 REMARK 3 2 3.5944 - 2.8537 0.97 1317 147 0.1904 0.2650 REMARK 3 3 2.8537 - 2.4932 0.96 1288 144 0.2307 0.3104 REMARK 3 4 2.4932 - 2.2653 0.93 1240 138 0.2305 0.3282 REMARK 3 5 2.2653 - 2.1030 0.87 1150 127 0.2484 0.2952 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 962 REMARK 3 ANGLE : 1.134 1304 REMARK 3 CHIRALITY : 0.046 142 REMARK 3 PLANARITY : 0.004 172 REMARK 3 DIHEDRAL : 16.938 346 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 5AI1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1290063020. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97960 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7126 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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: PDB ENTRY 1OPY REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE (PH 4.5), 0.6M REMARK 280 AMMONIUM ACETATE, 30% PEG 4,000, PH 4.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 36.76700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.76700 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 17.59750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.88450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 17.59750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.88450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 36.76700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 17.59750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.88450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 36.76700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 17.59750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.88450 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.7 KCAL/MOL 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 1 REMARK 465 GLY A 64 REMARK 465 LYS A 65 REMARK 465 TRP A 92 REMARK 465 ASN A 93 REMARK 465 GLY A 94 REMARK 465 GLN A 95 REMARK 465 ARG A 128 REMARK 465 GLU A 129 REMARK 465 PRO A 130 REMARK 465 GLN A 131 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 O HOH A 2042 O HOH A 2045 2.12 REMARK 500 OD2 ASP A 35 O HOH A 2022 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2042 O HOH A 2042 4555 1.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EQU A 1128 DBREF 5AI1 A 1 131 UNP P07445 SDIS_PSEPU 1 131 SEQADV 5AI1 PHE A 32 UNP P07445 TYR 32 ENGINEERED MUTATION SEQADV 5AI1 ASN A 40 UNP P07445 ASP 40 ENGINEERED MUTATION SEQADV 5AI1 PHE A 57 UNP P07445 TYR 57 ENGINEERED MUTATION SEQADV 5AI1 PHE A 119 UNP P07445 TYR 119 ENGINEERED MUTATION SEQRES 1 A 131 MET ASN LEU PRO THR ALA GLN GLU VAL GLN GLY LEU MET SEQRES 2 A 131 ALA ARG TYR ILE GLU LEU VAL ASP VAL GLY ASP ILE GLU SEQRES 3 A 131 ALA ILE VAL GLN MET PHE ALA ASP ASP ALA THR VAL GLU SEQRES 4 A 131 ASN PRO PHE GLY GLN PRO PRO ILE HIS GLY ARG GLU GLN SEQRES 5 A 131 ILE ALA ALA PHE PHE ARG GLN GLY LEU GLY GLY GLY LYS SEQRES 6 A 131 VAL ARG ALA CYS LEU THR GLY PRO VAL ARG ALA SER HIS SEQRES 7 A 131 ASN GLY CYS GLY ALA MET PRO PHE ARG VAL GLU MET VAL SEQRES 8 A 131 TRP ASN GLY GLN PRO CYS ALA LEU ASP VAL ILE ASP VAL SEQRES 9 A 131 MET ARG PHE ASP GLU HIS GLY ARG ILE GLN THR MET GLN SEQRES 10 A 131 ALA PHE TRP SER GLU VAL ASN LEU SER VAL ARG GLU PRO SEQRES 11 A 131 GLN HET EQU A1128 20 HETNAM EQU EQUILENIN FORMUL 2 EQU C18 H18 O2 FORMUL 3 HOH *58(H2 O) HELIX 1 1 THR A 5 GLY A 23 1 19 HELIX 2 2 ASP A 24 GLN A 30 1 7 HELIX 3 3 GLY A 49 GLY A 62 1 14 HELIX 4 4 SER A 121 VAL A 123 5 3 SHEET 1 AA 5 ILE A 47 HIS A 48 0 SHEET 2 AA 5 PHE A 32 GLU A 39 -1 O VAL A 38 N ILE A 47 SHEET 3 AA 5 ILE A 113 PHE A 119 1 O ILE A 113 N ALA A 33 SHEET 4 AA 5 CYS A 97 PHE A 107 -1 O ILE A 102 N PHE A 119 SHEET 5 AA 5 LEU A 125 SER A 126 -1 O SER A 126 N ALA A 98 SHEET 1 AB 6 ILE A 47 HIS A 48 0 SHEET 2 AB 6 PHE A 32 GLU A 39 -1 O VAL A 38 N ILE A 47 SHEET 3 AB 6 ILE A 113 PHE A 119 1 O ILE A 113 N ALA A 33 SHEET 4 AB 6 CYS A 97 PHE A 107 -1 O ILE A 102 N PHE A 119 SHEET 5 AB 6 CYS A 81 MET A 90 -1 O GLY A 82 N MET A 105 SHEET 6 AB 6 ARG A 75 ALA A 76 1 O ARG A 75 N ALA A 83 SHEET 1 AC 2 ARG A 67 LEU A 70 0 SHEET 2 AC 2 CYS A 81 MET A 90 -1 O ARG A 87 N CYS A 69 SHEET 1 AD 6 ILE A 47 HIS A 48 0 SHEET 2 AD 6 PHE A 32 GLU A 39 -1 O VAL A 38 N ILE A 47 SHEET 3 AD 6 ILE A 113 PHE A 119 1 O ILE A 113 N ALA A 33 SHEET 4 AD 6 CYS A 97 PHE A 107 -1 O ILE A 102 N PHE A 119 SHEET 5 AD 6 CYS A 81 MET A 90 -1 O GLY A 82 N MET A 105 SHEET 6 AD 6 ARG A 67 LEU A 70 -1 O ARG A 67 N GLU A 89 SHEET 1 AE 2 LEU A 125 SER A 126 0 SHEET 2 AE 2 CYS A 97 PHE A 107 -1 O ALA A 98 N SER A 126 CISPEP 1 ASN A 40 PRO A 41 0 -0.76 SITE 1 AC1 5 TYR A 16 ASN A 40 PHE A 86 MET A 90 SITE 2 AC1 5 ASP A 103 CRYST1 35.195 95.769 73.534 90.00 90.00 90.00 C 2 2 21 8 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 0.028413 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010442 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013599 0.00000