HEADER ISOMERASE 05-APR-13 4K1U TITLE CRYSTAL STRUCTURE OF DELTA5-3-KETOSTEROID ISOMERASE CONTAINING Y16F TITLE 2 AND Y32F MUTATIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: STEROID DELTA-ISOMERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DELTA(5)-3-KETOSTEROID ISOMERASE; COMPND 5 EC: 5.3.3.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 GENE: KSI; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYSTATIN-LIKE FOLD, ALLYLIC ISOMERIZATION, DELTA5-3KETOSTEROIDS, KEYWDS 2 CYTOSOL, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.J.CHA,D.S.JANG,Y.G.KIM,B.H.HONG,J.S.WOO,K.Y.CHOI REVDAT 3 20-MAR-24 4K1U 1 SEQADV REVDAT 2 04-SEP-13 4K1U 1 JRNL REVDAT 1 31-JUL-13 4K1U 0 JRNL AUTH H.J.CHA,D.S.JANG,Y.G.KIM,B.H.HONG,J.S.WOO,K.T.KIM,K.Y.CHOI JRNL TITL RESCUE OF DELETERIOUS MUTATIONS BY THE COMPENSATORY Y30F JRNL TITL 2 MUTATION IN KETOSTEROID ISOMERASE JRNL REF MOL.CELLS V. 36 39 2013 JRNL REFN ISSN 1016-8478 JRNL PMID 23740430 JRNL DOI 10.1007/S10059-013-0013-1 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 16120 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 786 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 : 1890 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL 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) : 1.464 REMARK 3 BOND ANGLES (DEGREES) : 2.335 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 4K1U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078784. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 6B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1271 REMARK 200 MONOCHROMATOR : DCM SI (111) CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16266 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 56.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.18400 REMARK 200 FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, AMMONIUM ACETATE, PH REMARK 280 4.60, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 17.14200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.54200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.54700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.54200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.14200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.54700 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 MET A 1 REMARK 465 GLY A 62 REMARK 465 GLY A 63 REMARK 465 GLY A 64 REMARK 465 LYS A 65 REMARK 465 ARG A 128 REMARK 465 GLU A 129 REMARK 465 PRO A 130 REMARK 465 GLN A 131 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 GLY B 62 REMARK 465 GLY B 63 REMARK 465 GLY B 64 REMARK 465 LYS B 65 REMARK 465 ARG B 128 REMARK 465 GLU B 129 REMARK 465 PRO B 130 REMARK 465 GLN B 131 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 VAL A 91 47.55 -96.35 REMARK 500 ASN A 93 38.93 75.55 REMARK 500 TRP A 120 153.93 176.19 REMARK 500 TRP B 120 158.85 175.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OPY RELATED DB: PDB REMARK 900 RELATED ID: 4K1V RELATED DB: PDB DBREF 4K1U A 1 131 UNP P07445 SDIS_PSEPU 1 131 DBREF 4K1U B 1 131 UNP P07445 SDIS_PSEPU 1 131 SEQADV 4K1U PHE A 16 UNP P07445 TYR 16 ENGINEERED MUTATION SEQADV 4K1U PHE A 32 UNP P07445 TYR 32 ENGINEERED MUTATION SEQADV 4K1U PHE B 16 UNP P07445 TYR 16 ENGINEERED MUTATION SEQADV 4K1U PHE B 32 UNP P07445 TYR 32 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 PHE 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 ASP PRO PHE GLY GLN PRO PRO ILE HIS GLY ARG GLU GLN SEQRES 5 A 131 ILE ALA ALA PHE TYR 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 TYR TRP SER GLU VAL ASN LEU SER VAL ARG GLU PRO SEQRES 11 A 131 GLN SEQRES 1 B 131 MET ASN LEU PRO THR ALA GLN GLU VAL GLN GLY LEU MET SEQRES 2 B 131 ALA ARG PHE ILE GLU LEU VAL ASP VAL GLY ASP ILE GLU SEQRES 3 B 131 ALA ILE VAL GLN MET PHE ALA ASP ASP ALA THR VAL GLU SEQRES 4 B 131 ASP PRO PHE GLY GLN PRO PRO ILE HIS GLY ARG GLU GLN SEQRES 5 B 131 ILE ALA ALA PHE TYR ARG GLN GLY LEU GLY GLY GLY LYS SEQRES 6 B 131 VAL ARG ALA CYS LEU THR GLY PRO VAL ARG ALA SER HIS SEQRES 7 B 131 ASN GLY CYS GLY ALA MET PRO PHE ARG VAL GLU MET VAL SEQRES 8 B 131 TRP ASN GLY GLN PRO CYS ALA LEU ASP VAL ILE ASP VAL SEQRES 9 B 131 MET ARG PHE ASP GLU HIS GLY ARG ILE GLN THR MET GLN SEQRES 10 B 131 ALA TYR TRP SER GLU VAL ASN LEU SER VAL ARG GLU PRO SEQRES 11 B 131 GLN FORMUL 3 HOH *94(H2 O) HELIX 1 1 THR A 5 GLY A 23 1 19 HELIX 2 2 ASP A 24 MET A 31 1 8 HELIX 3 3 GLY A 49 LEU A 61 1 13 HELIX 4 4 SER A 121 VAL A 123 5 3 HELIX 5 5 THR B 5 GLY B 23 1 19 HELIX 6 6 ASP B 24 MET B 31 1 8 HELIX 7 7 GLY B 49 LEU B 61 1 13 HELIX 8 8 SER B 121 VAL B 123 5 3 SHEET 1 A 6 ILE A 47 HIS A 48 0 SHEET 2 A 6 PHE A 32 GLU A 39 -1 N VAL A 38 O ILE A 47 SHEET 3 A 6 ILE A 113 TYR A 119 1 O ILE A 113 N ALA A 33 SHEET 4 A 6 CYS A 97 PHE A 107 -1 N ILE A 102 O TYR A 119 SHEET 5 A 6 CYS A 81 MET A 90 -1 N MET A 90 O CYS A 97 SHEET 6 A 6 ARG A 75 ALA A 76 -1 N ARG A 75 O ALA A 83 SHEET 1 B 4 ARG A 67 LEU A 70 0 SHEET 2 B 4 CYS A 81 MET A 90 -1 O GLU A 89 N ARG A 67 SHEET 3 B 4 CYS A 97 PHE A 107 -1 O CYS A 97 N MET A 90 SHEET 4 B 4 LEU A 125 SER A 126 -1 O SER A 126 N ALA A 98 SHEET 1 C 6 ILE B 47 HIS B 48 0 SHEET 2 C 6 PHE B 32 GLU B 39 -1 N VAL B 38 O ILE B 47 SHEET 3 C 6 ILE B 113 TYR B 119 1 O ILE B 113 N ALA B 33 SHEET 4 C 6 GLN B 95 PHE B 107 -1 N ILE B 102 O TYR B 119 SHEET 5 C 6 CYS B 81 TRP B 92 -1 N MET B 90 O CYS B 97 SHEET 6 C 6 ARG B 75 ALA B 76 -1 N ARG B 75 O ALA B 83 SHEET 1 D 4 ARG B 67 LEU B 70 0 SHEET 2 D 4 CYS B 81 TRP B 92 -1 O GLU B 89 N ARG B 67 SHEET 3 D 4 GLN B 95 PHE B 107 -1 O CYS B 97 N MET B 90 SHEET 4 D 4 LEU B 125 SER B 126 -1 O SER B 126 N ALA B 98 CISPEP 1 ASP A 40 PRO A 41 0 -0.10 CISPEP 2 ASP B 40 PRO B 41 0 0.01 CRYST1 34.284 73.094 95.084 90.00 90.00 90.00 P 21 21 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 0.029168 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013681 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010517 0.00000