HEADER ISOMERASE 29-OCT-97 4TSU OBSLTE 10-JUN-03 4TSU 1OH0 TITLE CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE COMPLEXED WITH TITLE 2 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: KETOSTEROID ISOMERASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 5.3.3.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 CELL_LINE: BL21; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 6 EXPRESSION_SYSTEM_PLASMID: BL21 KEYWDS ISOMERASE, INHIBITOR, COMPLEX, CRYSTAL, EXPDTA X-RAY DIFFRACTION AUTHOR S.-S.CHA,H.-S.CHO,J.-S.KIM,N.-C.HA,M.-J.CHO,B.-H.OH REVDAT 2 16-FEB-99 4TSU 3 SOURCE COMPND REMARK HETATM REVDAT 2 2 3 KEYWDS HEADER CONECT REVDAT 1 30-DEC-98 4TSU 0 JRNL AUTH S.W.KIM,S.S.CHA,H.S.CHO,J.S.KIM,N.C.HA,M.J.CHO, JRNL AUTH 2 S.JOO,K.K.KIM,K.Y.CHOI,B.H.OH JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURES OF JRNL TITL 2 DELTA5-3-KETOSTEROID ISOMERASE WITH AND WITHOUT A JRNL TITL 3 REACTION INTERMEDIATE ANALOGUE. JRNL REF BIOCHEMISTRY V. 36 14030 1997 JRNL REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.W.KIM,S.S.CHA,H.S.CHO,J.S.KIM,N.C.HA,M.J.CHO, REMARK 1 AUTH 2 S.JOO,K.K.KIM,K.Y.CHOI,B.H.OH REMARK 1 TITL ERRATUM. HIGH-RESOLUTION CRYSTAL STRUCTURES OF REMARK 1 TITL 2 DELTA5-3-KETOSTEROID ISOMERASE WITH AND WITHOUT A REMARK 1 TITL 3 REACTION INTERMEDIATE ANALOGUE REMARK 1 REF BIOCHEMISTRY V. 37 6614 1998 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH Z.R.WU,S.EBRAHIMIAN,M.E.ZAWROTNY,L.D.THORNBURG, REMARK 1 AUTH 2 G.C.PEREZ-ALVARADO,P.BROTHERS,R.M.POLLACK, REMARK 1 AUTH 3 M.F.SUMMERS REMARK 1 TITL SOLUTION STRUCTURE OF 3-OXO-DELTA5-STEROID REMARK 1 TITL 2 ISOMERASE REMARK 1 REF SCIENCE V. 276 415 1997 REMARK 1 REFN ASTM SCIEAS US ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.01 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 41282 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 977 REMARK 3 NUCLEIC ACID ATOMS : NULL REMARK 3 HETEROGEN ATOMS : NULL REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.50 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.74 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4TSU COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : DEC-1995 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 6.80 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : MAC SCIENCE M18XHF22 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : MAC SCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: UNINHIBITED KSI STRUCTURE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.8 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 1/2+X,1/2+Y,Z REMARK 290 4555 1/2-X,1/2+Y,-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 44.31000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.16500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.31000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.16500 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A 62 REMARK 465 GLY A 63 REMARK 465 GLY A 64 REMARK 465 ARG A 128 REMARK 465 GLU A 129 REMARK 465 PRO A 130 REMARK 465 GLN A 131 REMARK 465 GLY B 62 REMARK 465 GLY B 63 REMARK 465 GLY B 64 REMARK 465 ARG B 128 REMARK 465 GLU B 129 REMARK 465 PRO B 130 REMARK 465 GLN B 131 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 2 CG OD1 ND2 REMARK 470 ASN B 2 CG OD1 ND2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 4 C - N - CD ANGL. DEV. = 10.9 DEGREES REMARK 500 PHE A 42 N - CA - C ANGL. DEV. =-10.7 DEGREES REMARK 500 ILE A 47 N - CA - C ANGL. DEV. =-13.2 DEGREES REMARK 500 ALA B 33 N - CA - C ANGL. DEV. =-12.4 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 LEU A 3 -55.02 90.29 REMARK 500 ASN A 93 -54.36 68.27 REMARK 500 LEU B 3 -68.75 123.69 REMARK 860 REMARK 860 CORRECTION AFTER RELEASE REMARK 860 DATE: 16-FEB-99 REMARK 860 MODID: 4TSUA REMARK 860 MODIFIED BY: PDB REMARK 860 DESCRIPTION: CONVERTED FROM LAYER 1 OR NDB TO LAYER 2 REMARK 999 REMARK 999 SEQUENCE REMARK 999 4TSU A SWS P07445 1 - 1 NOT IN ATOMS LIST REMARK 999 4TSU A SWS P07445 128 - 131 NOT IN ATOMS LIST REMARK 999 4TSU B SWS P07445 1 - 1 NOT IN ATOMS LIST REMARK 999 4TSU B SWS P07445 128 - 131 NOT IN ATOMS LIST DBREF 4TSU A 2 131 UNP P07445 SDIS_PSEPU 2 131 DBREF 4TSU B 2 131 UNP P07445 SDIS_PSEPU 2 131 SEQRES 1 A 130 ASN LEU PRO THR ALA GLN GLU VAL GLN GLY LEU MET ALA SEQRES 2 A 130 ARG TYR ILE GLU LEU VAL ASP VAL GLY ASP ILE GLU ALA SEQRES 3 A 130 ILE VAL GLN MET TYR ALA ASP ASP ALA THR VAL GLU ASP SEQRES 4 A 130 PRO PHE GLY GLN PRO PRO ILE HIS GLY ARG GLU GLN ILE SEQRES 5 A 130 ALA ALA PHE TYR ARG GLN GLY LEU GLY GLY GLY LYS VAL SEQRES 6 A 130 ARG ALA CYS LEU THR GLY PRO VAL ARG ALA SER HIS ASN SEQRES 7 A 130 GLY CYS GLY ALA MET PRO PHE ARG VAL GLU MET VAL TRP SEQRES 8 A 130 ASN GLY GLN PRO CYS ALA LEU ASP VAL ILE ASP VAL MET SEQRES 9 A 130 ARG PHE ASP GLU HIS GLY ARG ILE GLN THR MET GLN ALA SEQRES 10 A 130 TYR TRP SER GLU VAL ASN LEU SER VAL ARG GLU PRO GLN SEQRES 1 B 130 ASN LEU PRO THR ALA GLN GLU VAL GLN GLY LEU MET ALA SEQRES 2 B 130 ARG TYR ILE GLU LEU VAL ASP VAL GLY ASP ILE GLU ALA SEQRES 3 B 130 ILE VAL GLN MET TYR ALA ASP ASP ALA THR VAL GLU ASP SEQRES 4 B 130 PRO PHE GLY GLN PRO PRO ILE HIS GLY ARG GLU GLN ILE SEQRES 5 B 130 ALA ALA PHE TYR ARG GLN GLY LEU GLY GLY GLY LYS VAL SEQRES 6 B 130 ARG ALA CYS LEU THR GLY PRO VAL ARG ALA SER HIS ASN SEQRES 7 B 130 GLY CYS GLY ALA MET PRO PHE ARG VAL GLU MET VAL TRP SEQRES 8 B 130 ASN GLY GLN PRO CYS ALA LEU ASP VAL ILE ASP VAL MET SEQRES 9 B 130 ARG PHE ASP GLU HIS GLY ARG ILE GLN THR MET GLN ALA SEQRES 10 B 130 TYR TRP SER GLU VAL ASN LEU SER VAL ARG GLU PRO GLN HET EQU 801 21 HET EQU 802 21 HETNAM EQU EQUILENIN FORMUL 3 EQU 2(C18 H18 O2) FORMUL 5 HOH *72(H2 O1) HELIX 1 1 ALA A 6 VAL A 22 1 17 HELIX 2 2 ILE A 25 MET A 31 1 7 HELIX 3 3 GLY A 49 GLY A 60 1 12 HELIX 4 4 GLU A 122 ASN A 124 5 3 HELIX 5 5 ALA B 6 VAL B 22 1 17 HELIX 6 6 ILE B 25 MET B 31 1 7 HELIX 7 7 GLY B 49 GLY B 60 1 12 HELIX 8 8 GLU B 122 ASN B 124 5 3 SHEET 1 A 5 THR A 37 GLU A 39 0 SHEET 2 A 5 ILE A 113 TYR A 119 1 N MET A 116 O THR A 37 SHEET 3 A 5 GLN A 95 PHE A 107 -1 N ARG A 106 O GLN A 114 SHEET 4 A 5 CYS A 81 TRP A 92 -1 N TRP A 92 O GLN A 95 SHEET 5 A 5 ARG A 67 LEU A 70 -1 N CYS A 69 O ARG A 87 SHEET 1 B 5 THR B 37 GLU B 39 0 SHEET 2 B 5 ILE B 113 TYR B 119 1 N MET B 116 O THR B 37 SHEET 3 B 5 GLN B 95 PHE B 107 -1 N ARG B 106 O GLN B 114 SHEET 4 B 5 CYS B 81 TRP B 92 -1 N TRP B 92 O GLN B 95 SHEET 5 B 5 ARG B 67 LEU B 70 -1 N CYS B 69 O ARG B 87 CISPEP 1 ASP A 40 PRO A 41 0 0.38 CISPEP 2 ASP B 40 PRO B 41 0 -0.29 CRYST1 88.620 72.330 51.180 90.00 90.67 90.00 C 1 2 1 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 0.011284 0.000000 0.000132 0.00000 SCALE2 0.000000 0.013826 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019540 0.00000