HEADER OXIDOREDUCTASE 03-JAN-01 1HU4 OBSLTE 13-NOV-02 1HU4 1N5D TITLE CRYSTAL STRUCTURE OF PORCINE TESTICULAR CARBONYL REDUCTASE/ TITLE 2 20BETA-HYDROXYSTEROID DEHYDROGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBONYL REDUCTASE/20BETA-HYDROXYSTEROID COMPND 3 DEHYDROGENASE; COMPND 4 CHAIN: A; COMPND 5 EC: 1.1.1.53 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA; SOURCE 3 ORGANISM_COMMON: PIG KEYWDS SHORTCHAIN DEHYDROGENASE/REDUCTASE, MONOMER, NADP-COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.GHOSH REVDAT 3 01-APR-03 1HU4 1 JRNL REVDAT 2 13-NOV-02 1HU4 1 OBSLTE REVDAT 1 18-JUL-01 1HU4 0 JRNL AUTH D.GHOSH,M.SAWICKI,V.PLETNEV,M.ERMAN,S.OHNO, JRNL AUTH 2 S.NAKAJIN,W.L.DUAX JRNL TITL PORCINE CARBONYL REDUCTASE. STRUCTURAL BASIS FOR A JRNL TITL 2 FUNCTIONAL MONOMER IN SHORT CHAIN JRNL TITL 3 DEHYDROGENASES/REDUCTASES. JRNL REF J.BIOL.CHEM. V. 276 18457 2001 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.GHOSH,M.ERMAN,W.PANGBORN,W.L.DUAX,S.NAKAJIN, REMARK 1 AUTH 2 S.OHNO,M.SHINODA REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION REMARK 1 TITL 2 STUDIES OF A MAMMALIAN STEROID DEHYDROGENASE REMARK 1 REF J.STEROID BIOCHEM.MOL.BIOL. V. 46 103 1993 REMARK 1 REFN ASTM JSBBEZ UK ISSN 0960-0760 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 AND HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 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 : 10792 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) : 0.194 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 540 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 : 2219 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 58 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.00 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) : 0.35 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) : 0.37 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.62 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 1HU4 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-2001. REMARK 100 THE RCSB ID CODE IS RCSB012589. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-1992 REMARK 200 TEMPERATURE (KELVIN) : 280.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU 200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MONOCHROMATORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 52.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,1/2+Z REMARK 290 3555 1/2-Y,1/2+X,3/4+Z REMARK 290 4555 1/2+Y,1/2-X,1/4+Z REMARK 290 5555 1/2-X,1/2+Y,3/4-Z REMARK 290 6555 1/2+X,1/2-Y,1/4-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,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 82.82000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.26500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.26500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 124.23000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.26500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.26500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 41.41000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.26500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.26500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 124.23000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.26500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.26500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 41.41000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 82.82000 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 1 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 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 110 SD MET A 110 CE -0.127 REMARK 500 THR A 112 CB THR A 112 CG2 -0.049 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 GLN A 27 N - CA - C ANGL. DEV. = 7.8 DEGREES REMARK 500 ASP A 62 N - CA - C ANGL. DEV. =-10.4 DEGREES REMARK 500 ASN A 98 N - CA - C ANGL. DEV. = -8.8 DEGREES REMARK 500 PHE A 267 N - CA - C ANGL. DEV. = -7.8 DEGREES DBREF 1HU4 A 1 288 GB 164294 AAA30980 2 289 SEQRES 1 A 288 SER SER ASN THR ARG VAL ALA LEU VAL THR GLY ALA ASN SEQRES 2 A 288 LYS GLY ILE GLY PHE ALA ILE VAL ARG ASP LEU CYS ARG SEQRES 3 A 288 GLN PHE ALA GLY ASP VAL VAL LEU THR ALA ARG ASP VAL SEQRES 4 A 288 ALA ARG GLY GLN ALA ALA VAL LYS GLN LEU GLN ALA GLU SEQRES 5 A 288 GLY LEU SER PRO ARG PHE HIS GLN LEU ASP ILE ILE ASP SEQRES 6 A 288 LEU GLN SER ILE ARG ALA LEU CYS ASP PHE LEU ARG LYS SEQRES 7 A 288 GLU TYR GLY GLY LEU ASP VAL LEU VAL ASN ASN ALA ALA SEQRES 8 A 288 ILE ALA PHE GLN LEU ASP ASN PRO THR PRO PHE HIS ILE SEQRES 9 A 288 GLN ALA GLU LEU THR MET LYS THR ASN PHE MET GLY THR SEQRES 10 A 288 ARG ASN VAL CYS THR GLU LEU LEU PRO LEU ILE LYS PRO SEQRES 11 A 288 GLN GLY ARG VAL VAL ASN VAL SER SER THR GLU GLY VAL SEQRES 12 A 288 ARG ALA LEU ASN GLU CYS SER PRO GLU LEU GLN GLN LYS SEQRES 13 A 288 PHE LYS SER GLU THR ILE THR GLU GLU GLU LEU VAL GLY SEQRES 14 A 288 LEU MET ASN LYS PHE VAL GLU ASP THR LYS ASN GLY VAL SEQRES 15 A 288 HIS ARG LYS GLU GLY TRP SER ASP SER THR TYR GLY VAL SEQRES 16 A 288 THR LYS ILE GLY VAL SER VAL LEU SER ARG ILE TYR ALA SEQRES 17 A 288 ARG LYS LEU ARG GLU GLN ARG ALA GLY ASP LYS ILE LEU SEQRES 18 A 288 LEU ASN ALA CYS CYS PRO GLY TRP VAL ARG THR ASP MET SEQRES 19 A 288 GLY GLY PRO LYS ALA PRO LYS SER PRO GLU VAL GLY ALA SEQRES 20 A 288 GLU THR PRO VAL TYR LEU ALA LEU LEU PRO SER ASP ALA SEQRES 21 A 288 GLU GLY PRO HIS GLY GLN PHE VAL THR ASP LYS LYS VAL SEQRES 22 A 288 VAL GLU TRP GLY VAL PRO PRO GLU SER TYR PRO TRP VAL SEQRES 23 A 288 ASN ALA HET SO4 400 5 HET NDP 300 48 HETNAM SO4 SULFATE ION HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE FORMUL 2 SO4 O4 S 2- FORMUL 3 NDP C21 H30 N7 O17 P3 FORMUL 4 HOH *58(H2 O1) HELIX 1 1 LYS A 14 PHE A 28 1 15 HELIX 2 2 ASP A 38 ALA A 51 1 14 HELIX 3 3 ASP A 65 GLY A 81 1 17 HELIX 4 4 PRO A 101 PHE A 114 1 14 HELIX 5 5 PHE A 114 LEU A 125 1 12 HELIX 6 6 THR A 140 CYS A 149 1 10 HELIX 7 7 SER A 150 LYS A 158 1 9 HELIX 8 8 THR A 163 ASN A 180 1 18 HELIX 9 9 SER A 191 ARG A 215 1 25 HELIX 10 10 ALA A 216 LYS A 219 5 4 HELIX 11 11 SER A 242 ALA A 247 1 6 HELIX 12 12 ALA A 247 LEU A 255 1 9 SHEET 1 A 8 ARG A 57 GLN A 60 0 SHEET 2 A 8 ASP A 31 ALA A 36 1 O VAL A 32 N ARG A 57 SHEET 3 A 8 VAL A 6 VAL A 9 1 O ALA A 7 N VAL A 33 SHEET 4 A 8 LEU A 83 ASN A 88 1 N ASP A 84 O VAL A 6 SHEET 5 A 8 ILE A 128 VAL A 137 1 N LYS A 129 O LEU A 83 SHEET 6 A 8 LEU A 221 CYS A 226 1 O LEU A 221 N VAL A 134 SHEET 7 A 8 PHE A 267 THR A 269 1 N VAL A 268 O ALA A 224 SHEET 8 A 8 LYS A 272 VAL A 273 -1 O LYS A 272 N THR A 269 CISPEP 1 GLY A 262 PRO A 263 0 -0.18 CRYST1 58.530 58.530 165.640 90.00 90.00 90.00 P 43 21 2 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 0.017085 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017085 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006037 0.00000