HEADER OXIDOREDUCTASE 03-MAY-12 4AT2 TITLE THE CRYSTAL STRUCTURE OF 3-KETOSTEROID-DELTA4-(5ALPHA)- TITLE 2 DEHYDROGENASE FROM RHODOCOCCUS JOSTII RHA1 IN COMPLEX TITLE 3 WITH 4-ANDROSTENE-3,17- DIONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-KETOSTEROID-DELTA4-5ALPHA-DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.3.99.5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOCOCCUS JOSTII; SOURCE 3 ORGANISM_TAXID: 101510; SOURCE 4 STRAIN: RHA1; 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: PET15B KEYWDS OXIDOREDUCTASE, STEROID CATABOLISM EXPDTA X-RAY DIFFRACTION AUTHOR N.VAN OOSTERWIJK,J.KNOL,L.DIJKHUIZEN,R.VAN DER GEIZE,B.W.DIJKSTRA REVDAT 2 10-OCT-12 4AT2 1 JRNL REVDAT 1 01-AUG-12 4AT2 0 JRNL AUTH N.VAN OOSTERWIJK,J.KNOL,L.DIJKHUIZEN,R.VAN DER GEIZE, JRNL AUTH 2 B.W.DIJKSTRA JRNL TITL STRUCTURE AND CATALYTIC MECHANISM OF 3-KETOSTEROID-{DELTA}4- JRNL TITL 2 (5ALPHA)-DEHYDROGENASE FROM RHODOCOCCUS JOSTII RHA1 GENOME. JRNL REF J.BIOL.CHEM. V. 287 30975 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22833669 JRNL DOI 10.1074/JBC.M112.374306 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.600 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.367 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 95.020 REMARK 3 NUMBER OF REFLECTIONS : 80066 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.1593 REMARK 3 FREE R VALUE : 0.1806 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.08 REMARK 3 FREE R VALUE TEST SET COUNT : 4018 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.6 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.642 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3884 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.831 REMARK 3 BIN R VALUE (WORKING SET) : 0.225 REMARK 3 BIN FREE R VALUE SET COUNT : 174 REMARK 3 BIN FREE R VALUE : 0.254 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3660 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 75 REMARK 3 SOLVENT ATOMS : 618 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.2 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.916 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.418 REMARK 3 B22 (A**2) : 0.173 REMARK 3 B33 (A**2) : -0.591 REMARK 3 B12 (A**2) : 0.000 REMARK 3 B13 (A**2) : 0.000 REMARK 3 B23 (A**2) : 0.000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.072 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.270 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3832 ; 0.007 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5236 ; 1.251 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 504 ; 5.179 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 162 ;34.782 ;23.951 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 580 ;11.469 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;12.977 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 568 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2980 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2640 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2670 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 143 ; 0.090 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 100 ; 0.236 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.101 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3831 ; 0.701 ; 1.053 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5229 ; 1.183 ; 1.562 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1271 ; 2.510 ; 3.253 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 5438 ; 5.246 ; 5.908 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 489 REMARK 3 ORIGIN FOR THE GROUP (A): 39.7500 22.6230 41.5280 REMARK 3 T TENSOR REMARK 3 T11: 0.0101 T22: 0.0255 REMARK 3 T33: 0.0153 T12: 0.0036 REMARK 3 T13: -0.0078 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 0.0962 L22: 0.5013 REMARK 3 L33: 0.1332 L12: -0.0761 REMARK 3 L13: -0.0201 L23: -0.0083 REMARK 3 S TENSOR REMARK 3 S11: -0.0252 S12: -0.0063 S13: 0.0239 REMARK 3 S21: 0.0401 S22: 0.0188 S23: 0.0215 REMARK 3 S31: -0.0076 S32: -0.0476 S33: 0.0064 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PLUS MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.400 REMARK 3 ION PROBE RADIUS : 0.800 REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 4AT2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-MAY-12. REMARK 100 THE PDBE ID CODE IS EBI-52355. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-07 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 : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD (QUANTUM 210) REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80072 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.60 REMARK 200 RESOLUTION RANGE LOW (A) : 51.35 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NONE REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 4.88 REMARK 200 R MERGE (I) : 0.11 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.50 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.28 REMARK 200 R MERGE FOR SHELL (I) : 0.37 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.20 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE OBTAINED FROM 200 REMARK 280 MM AMMONIUM ACETATE, 100 MM SODIUM CITRATE PH 5.6 AND REMARK 280 30%(W/V) PEG 4000 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 55.07550 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 55.07550 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 49.88900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 58.04100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 49.88900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.04100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 55.07550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 49.88900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 58.04100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 55.07550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 49.88900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 58.04100 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 300 DETAILS: THE BIOLOGICAL UNIT IS UNDETERMINED BY THE AUTHOR 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.8 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 99.77800 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 55.07550 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2179 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2391 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2394 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2418 LIES ON A SPECIAL POSITION. 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 VAL A 2 REMARK 465 ASP A 3 REMARK 465 ALA A 4 REMARK 465 THR A 5 REMARK 465 PRO A 6 REMARK 465 ALA A 490 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 2179 O HOH A 2179 3655 0.33 REMARK 500 O HOH A 2391 O HOH A 2391 3655 1.24 REMARK 500 O HOH A 2418 O HOH A 2418 3655 0.67 REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 29 55.06 -107.81 REMARK 500 PHE A 140 -160.54 -114.58 REMARK 500 GLU A 177 -50.43 -128.28 REMARK 500 LYS A 178 80.60 -168.44 REMARK 500 ALA A 239 36.92 -147.44 REMARK 500 TYR A 313 -11.23 -146.20 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 ASD A1490 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1491 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A1492 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4AT0 RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF 3-KETOSTEROID-DELTA4-(5ALPHA)- REMARK 900 DEHYDROGENASE FROM RHODOCOCCUS JOSTII RHA1 REMARK 999 REMARK 999 SEQUENCE REMARK 999 TWO POINT MUTATIONS, COMPARED TO THE DATABASE SEQUENCE, REMARK 999 WERE FOUND IN THE STRUCTURE. A60T AND T160A, AND CONFIRMED REMARK 999 BY SEQUENCING OF THE CONSTRUCT. A HIS6-TAG AND LINKER, REMARK 999 MGSSHHHHHHSSGLVPRGSH, WAS ADDED TO THE PROTEIN. DBREF 4AT2 A 1 490 UNP Q0S4Q9 Q0S4Q9_RHOSR 1 490 SEQADV 4AT2 MET A -19 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 GLY A -18 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 SER A -17 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 SER A -16 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 HIS A -15 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 HIS A -14 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 HIS A -13 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 HIS A -12 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 HIS A -11 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 HIS A -10 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 SER A -9 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 SER A -8 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 GLY A -7 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 LEU A -6 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 VAL A -5 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 PRO A -4 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 ARG A -3 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 GLY A -2 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 SER A -1 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 HIS A 0 UNP Q0S4Q9 EXPRESSION TAG SEQADV 4AT2 THR A 60 UNP Q0S4Q9 ALA 60 SEE REMARK 999 SEQADV 4AT2 ALA A 160 UNP Q0S4Q9 THR 160 SEE REMARK 999 SEQRES 1 A 510 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 510 LEU VAL PRO ARG GLY SER HIS MET VAL ASP ALA THR PRO SEQRES 3 A 510 ILE ARG PRO ARG SER ALA THR THR VAL THR GLU TRP ASP SEQRES 4 A 510 TYR GLU ALA ASP VAL VAL VAL ALA GLY TYR GLY ILE ALA SEQRES 5 A 510 GLY VAL ALA ALA SER ILE GLU ALA ALA ARG ALA GLY ALA SEQRES 6 A 510 ASP VAL LEU VAL LEU GLU ARG THR SER GLY TRP GLY GLY SEQRES 7 A 510 ALA THR ALA LEU ALA GLY GLY PHE ILE TYR LEU GLY GLY SEQRES 8 A 510 GLY THR PRO LEU GLN LYS ALA CYS GLY PHE ASP ASP SER SEQRES 9 A 510 PRO GLU ASN MET LYS THR PHE MET MET ALA ALA LEU GLY SEQRES 10 A 510 PRO GLY ALA ASP GLU GLU LYS ILE THR ASP TYR CYS GLU SEQRES 11 A 510 GLY SER VAL GLU HIS TYR ASN TRP LEU VAL ASP CYS GLY SEQRES 12 A 510 VAL PRO PHE LYS GLU SER PHE TRP GLY GLU PRO GLY TRP SEQRES 13 A 510 GLU PRO PRO PHE ASP ASP GLY LEU MET TYR SER GLY GLY SEQRES 14 A 510 GLU ASN ALA ALA PRO PHE ASN GLU ILE ALA ALA PRO ALA SEQRES 15 A 510 PRO ARG GLY HIS VAL PRO GLN MET ASP GLY LYS ARG THR SEQRES 16 A 510 GLY GLU LYS GLY GLY GLY TYR MET LEU MET LYS PRO LEU SEQRES 17 A 510 VAL GLU THR ALA GLU LYS LEU GLY VAL ARG ALA GLU TYR SEQRES 18 A 510 ASP MET ARG VAL GLN THR LEU VAL THR ASP ASP THR GLY SEQRES 19 A 510 ARG VAL VAL GLY ILE VAL ALA LYS GLN TYR GLY LYS GLU SEQRES 20 A 510 VAL ALA VAL ARG ALA ARG ARG GLY VAL VAL LEU ALA THR SEQRES 21 A 510 GLY SER PHE ALA TYR ASN ASP LYS MET ILE GLU ALA HIS SEQRES 22 A 510 ALA PRO ARG LEU ILE GLY ARG PRO GLY ALA ALA ILE GLU SEQRES 23 A 510 GLU HIS ASP GLY ARG SER ILE LEU MET ALA GLN ALA LEU SEQRES 24 A 510 GLY ALA ASP LEU ALA HIS MET ASP ALA THR GLU VAL ALA SEQRES 25 A 510 PHE VAL CYS ASP PRO GLN LEU ILE VAL ARG GLY ILE LEU SEQRES 26 A 510 VAL ASN GLY ARG GLY GLN ARG TYR VAL PRO GLU ASP THR SEQRES 27 A 510 TYR SER GLY ARG ILE GLY GLN MET THR LEU PHE HIS GLN SEQRES 28 A 510 ASP ASN GLN ALA PHE LEU ILE ILE ASP GLU ALA SER TYR SEQRES 29 A 510 GLU GLU GLY ALA ALA ALA THR THR ALA THR PRO PHE LEU SEQRES 30 A 510 ARG VAL GLN PRO LYS TRP ALA ALA GLU THR VAL GLU GLU SEQRES 31 A 510 LEU GLU SER ASP MET GLY LEU PRO ALA GLY ALA LEU GLN SEQRES 32 A 510 SER THR VAL GLU VAL TYR ASN LYS HIS ALA ALA GLU GLY SEQRES 33 A 510 SER ASP PRO LEU LEU HIS LYS LYS SER GLU TRP VAL LYS SEQRES 34 A 510 PRO ILE GLY THR PRO VAL ALA ALA LEU ASP LEU ARG GLY SEQRES 35 A 510 PHE THR LEU GLY PHE THR LEU GLY GLY LEU ARG THR THR SEQRES 36 A 510 VAL ASN SER GLU VAL LEU HIS VAL SER GLY GLU PRO ILE SEQRES 37 A 510 PRO GLY LEU PHE ALA ALA GLY ARG CYS THR SER GLY VAL SEQRES 38 A 510 CYS ALA GLY GLY TYR ALA SER GLY THR SER LEU GLY ASP SEQRES 39 A 510 GLY SER PHE TYR GLY ARG ARG ALA GLY ILE SER ALA ALA SEQRES 40 A 510 LYS GLN ALA HET ASD A1490 21 HET CL A1491 1 HET FAD A1492 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM ASD 4-ANDROSTENE-3-17-DIONE HETNAM CL CHLORIDE ION FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 ASD C19 H26 O2 FORMUL 4 CL CL 1- FORMUL 5 HOH *618(H2 O) HELIX 1 1 THR A 13 VAL A 15 5 3 HELIX 2 2 GLY A 30 ALA A 43 1 14 HELIX 3 3 ALA A 59 ALA A 63 5 5 HELIX 4 4 THR A 73 CYS A 79 1 7 HELIX 5 5 SER A 84 LEU A 96 1 13 HELIX 6 6 ASP A 101 GLY A 111 1 11 HELIX 7 7 GLY A 111 CYS A 122 1 12 HELIX 8 8 PRO A 154 ILE A 158 5 5 HELIX 9 9 GLY A 181 LEU A 195 1 15 HELIX 10 10 ASN A 246 ALA A 254 1 9 HELIX 11 11 PRO A 255 ILE A 258 5 4 HELIX 12 12 GLY A 270 ALA A 278 1 9 HELIX 13 13 ASP A 296 VAL A 301 1 6 HELIX 14 14 TYR A 319 GLN A 331 1 13 HELIX 15 15 GLU A 341 ALA A 350 1 10 HELIX 16 16 THR A 354 ARG A 358 5 5 HELIX 17 17 THR A 367 MET A 375 1 9 HELIX 18 18 GLY A 380 ALA A 394 1 15 HELIX 19 19 LYS A 404 VAL A 408 5 5 HELIX 20 20 GLY A 469 LYS A 488 1 20 SHEET 1 AA 6 ARG A 10 SER A 11 0 SHEET 2 AA 6 MET A 203 THR A 210 1 O LEU A 208 N ARG A 10 SHEET 3 AA 6 VAL A 216 GLN A 223 -1 N VAL A 217 O VAL A 209 SHEET 4 AA 6 LYS A 226 LEU A 238 -1 O LYS A 226 N GLN A 223 SHEET 5 AA 6 PRO A 447 ALA A 453 -1 O GLY A 450 N VAL A 236 SHEET 6 AA 6 GLU A 439 LEU A 441 1 O VAL A 440 N ILE A 448 SHEET 1 AB 7 ARG A 10 SER A 11 0 SHEET 2 AB 7 MET A 203 THR A 210 1 O LEU A 208 N ARG A 10 SHEET 3 AB 7 VAL A 216 GLN A 223 -1 N VAL A 217 O VAL A 209 SHEET 4 AB 7 LYS A 226 LEU A 238 -1 O LYS A 226 N GLN A 223 SHEET 5 AB 7 TYR A 20 ALA A 27 1 O TYR A 20 N ARG A 231 SHEET 6 AB 7 VAL A 47 LEU A 50 1 O LEU A 48 N VAL A 26 SHEET 7 AB 7 ARG A 198 GLU A 200 1 O ARG A 198 N VAL A 49 SHEET 1 AC 3 ILE A 67 TYR A 68 0 SHEET 2 AC 3 GLY A 165 HIS A 166 -1 O HIS A 166 N ILE A 67 SHEET 3 AC 3 LEU A 144 MET A 145 -1 O MET A 145 N GLY A 165 SHEET 1 AD 2 LEU A 283 ALA A 284 0 SHEET 2 AD 2 GLY A 431 LEU A 432 -1 O GLY A 431 N ALA A 284 SHEET 1 AE 2 THR A 289 PHE A 293 0 SHEET 2 AE 2 THR A 424 THR A 428 -1 O LEU A 425 N ALA A 292 SHEET 1 AF 4 ILE A 304 VAL A 306 0 SHEET 2 AF 4 PHE A 336 ASP A 340 -1 O PHE A 336 N VAL A 306 SHEET 3 AF 4 VAL A 415 ASP A 419 -1 O ALA A 416 N ILE A 339 SHEET 4 AF 4 TRP A 363 ALA A 365 -1 O TRP A 363 N ALA A 417 CISPEP 1 GLY A 97 PRO A 98 0 4.16 CISPEP 2 ALA A 153 PRO A 154 0 -0.79 CISPEP 3 THR A 413 PRO A 414 0 -4.73 SITE 1 AC1 10 TRP A 136 GLU A 290 ALA A 292 TYR A 319 SITE 2 AC1 10 TYR A 466 SER A 468 GLY A 469 FAD A1492 SITE 3 AC1 10 HOH A2616 HOH A2617 SITE 1 AC2 2 ALA A 264 HOH A2618 SITE 1 AC3 41 GLY A 28 GLY A 30 ILE A 31 ALA A 32 SITE 2 AC3 41 LEU A 50 GLU A 51 ARG A 52 THR A 53 SITE 3 AC3 41 GLY A 58 ALA A 59 THR A 60 ALA A 63 SITE 4 AC3 41 GLY A 64 GLY A 65 PHE A 66 THR A 175 SITE 5 AC3 41 MET A 203 VAL A 205 ALA A 239 THR A 240 SITE 6 AC3 41 GLY A 241 GLY A 262 ILE A 265 GLU A 267 SITE 7 AC3 41 HIS A 268 PHE A 427 GLY A 455 ARG A 456 SITE 8 AC3 41 TYR A 466 GLY A 469 THR A 470 SER A 471 SITE 9 AC3 41 LEU A 472 ASD A1490 HOH A2034 HOH A2079 SITE 10 AC3 41 HOH A2086 HOH A2103 HOH A2366 HOH A2602 SITE 11 AC3 41 HOH A2618 CRYST1 99.778 116.082 110.151 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 0.010022 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008615 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009078 0.00000