HEADER OXIDOREDUCTASE 12-APR-12 3VRM TITLE STRUCTURE OF CYTOCHROME P450 VDH MUTANT T107A WITH BOUND VITAMIN D3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN D(3) 25-HYDROXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOCHROME P450; COMPND 5 EC: 1.14.13.15; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDONOCARDIA AUTOTROPHICA; SOURCE 3 ORGANISM_COMMON: AMYCOLATA AUTOTROPHICA; SOURCE 4 ORGANISM_TAXID: 2074; SOURCE 5 STRAIN: NBRC 12743; SOURCE 6 GENE: VDH; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET22 KEYWDS CYTOCHROME P450, VITAMIN D3, MONOOXYGENASE, OXIDOREDUCTASE, P450 KEYWDS 2 FOLD, HEMOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.NISHIOKA,Y.YASUTAKE,T.TAMURA REVDAT 3 08-NOV-23 3VRM 1 COMPND REMARK SEQADV HETNAM REVDAT 2 27-NOV-13 3VRM 1 JRNL REVDAT 1 17-APR-13 3VRM 0 JRNL AUTH Y.YASUTAKE,T.NISHIOKA,N.IMOTO,T.TAMURA JRNL TITL A SINGLE MUTATION AT THE FERREDOXIN BINDING SITE OF P450 VDH JRNL TITL 2 ENABLES EFFICIENT BIOCATALYTIC PRODUCTION OF JRNL TITL 3 25-HYDROXYVITAMIN D3. JRNL REF CHEMBIOCHEM V. 14 2284 2013 JRNL REFN ISSN 1439-4227 JRNL PMID 24115473 JRNL DOI 10.1002/CBIC.201300386 REMARK 2 REMARK 2 RESOLUTION. 2.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 14156 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 741 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) : 2.57 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 805 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 33 REMARK 3 BIN FREE R VALUE : 0.4230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3105 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 71 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 68.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 76.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.43000 REMARK 3 B22 (A**2) : 6.74000 REMARK 3 B33 (A**2) : -3.31000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.807 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.290 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.264 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 23.368 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3281 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4485 ; 1.934 ; 2.025 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 401 ; 5.644 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;29.650 ;23.217 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 519 ;18.226 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;20.473 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 503 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2509 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 100 REMARK 3 RESIDUE RANGE : A 101 A 239 REMARK 3 RESIDUE RANGE : A 240 A 403 REMARK 3 ORIGIN FOR THE GROUP (A): 11.2528 24.5383 17.9473 REMARK 3 T TENSOR REMARK 3 T11: 0.0779 T22: 0.1908 REMARK 3 T33: 0.0462 T12: -0.0087 REMARK 3 T13: -0.0003 T23: 0.0163 REMARK 3 L TENSOR REMARK 3 L11: 4.7688 L22: 1.4214 REMARK 3 L33: 4.1456 L12: 0.3654 REMARK 3 L13: 2.6227 L23: 0.5316 REMARK 3 S TENSOR REMARK 3 S11: 0.0198 S12: -0.5803 S13: -0.0278 REMARK 3 S21: 0.2973 S22: 0.0210 S23: 0.0805 REMARK 3 S31: -0.0239 S32: -0.2321 S33: -0.0408 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE REMARK 3 INPUT REMARK 4 REMARK 4 3VRM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000095414. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14156 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.570 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.55700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.050 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: PDB ENTRY 3A50 REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 3350, 0.2M NACL, 0.1M BIS REMARK 280 -TRIS, PH 6.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 70.99400 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 70.99400 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 30.71050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.76050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.71050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.76050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 70.99400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.71050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 52.76050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 70.99400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.71050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 52.76050 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: MONOMERIC 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 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 LEU A 404 REMARK 465 GLU A 405 REMARK 465 HIS A 406 REMARK 465 HIS A 407 REMARK 465 HIS A 408 REMARK 465 HIS A 409 REMARK 465 HIS A 410 REMARK 465 HIS A 411 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 GLU A 9 110.39 -165.23 REMARK 500 PHE A 14 34.25 71.58 REMARK 500 ASP A 33 63.30 -156.68 REMARK 500 ASP A 42 44.48 -107.06 REMARK 500 TYR A 51 -73.59 -53.62 REMARK 500 GLU A 73 -51.63 -25.09 REMARK 500 PRO A 85 60.00 -67.59 REMARK 500 TYR A 141 -60.70 -149.55 REMARK 500 ALA A 158 0.90 -68.37 REMARK 500 ASP A 203 -163.91 -122.65 REMARK 500 ASP A 217 77.73 -158.50 REMARK 500 GLU A 239 8.60 -59.18 REMARK 500 THR A 240 -58.06 -122.71 REMARK 500 ASP A 294 130.79 -33.41 REMARK 500 SER A 298 37.19 35.20 REMARK 500 PRO A 303 160.25 -47.69 REMARK 500 PHE A 346 130.68 -33.25 REMARK 500 CYS A 347 120.76 -37.97 REMARK 500 LEU A 387 -38.46 -134.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 347 SG REMARK 620 2 HEM A 501 NA 118.1 REMARK 620 3 HEM A 501 NB 88.0 86.8 REMARK 620 4 HEM A 501 NC 96.1 145.5 89.9 REMARK 620 5 HEM A 501 ND 111.6 83.5 160.5 88.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VD3 A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A4G RELATED DB: PDB REMARK 900 WILD-TYPE VDH REMARK 900 RELATED ID: 3A4H RELATED DB: PDB REMARK 900 WILD-TYPE VDH REMARK 900 RELATED ID: 3A4Z RELATED DB: PDB REMARK 900 HIGHLY ACTIVE VDH MUTANT BY DIRECTED EVOLUTION REMARK 900 RELATED ID: 3A50 RELATED DB: PDB REMARK 900 HIGHLY ACTIVE VDH MUTANT BY DIRECTED EVOLUTION REMARK 900 RELATED ID: 3A51 RELATED DB: PDB REMARK 900 HIGHLY ACTIVE VDH MUTANT BY DIRECTED EVOLUTION DBREF 3VRM A 1 403 UNP C4B644 CPVDH_PSEAH 1 403 SEQADV 3VRM ALA A 107 UNP C4B644 THR 107 ENGINEERED MUTATION SEQADV 3VRM LEU A 404 UNP C4B644 EXPRESSION TAG SEQADV 3VRM GLU A 405 UNP C4B644 EXPRESSION TAG SEQADV 3VRM HIS A 406 UNP C4B644 EXPRESSION TAG SEQADV 3VRM HIS A 407 UNP C4B644 EXPRESSION TAG SEQADV 3VRM HIS A 408 UNP C4B644 EXPRESSION TAG SEQADV 3VRM HIS A 409 UNP C4B644 EXPRESSION TAG SEQADV 3VRM HIS A 410 UNP C4B644 EXPRESSION TAG SEQADV 3VRM HIS A 411 UNP C4B644 EXPRESSION TAG SEQRES 1 A 411 MET ALA LEU THR THR THR GLY THR GLU GLN HIS ASP LEU SEQRES 2 A 411 PHE SER GLY THR PHE TRP GLN ASN PRO HIS PRO ALA TYR SEQRES 3 A 411 ALA ALA LEU ARG ALA GLU ASP PRO VAL ARG LYS LEU ALA SEQRES 4 A 411 LEU PRO ASP GLY PRO VAL TRP LEU LEU THR ARG TYR ALA SEQRES 5 A 411 ASP VAL ARG GLU ALA PHE VAL ASP PRO ARG LEU SER LYS SEQRES 6 A 411 ASP TRP ARG HIS THR LEU PRO GLU ASP GLN ARG ALA ASP SEQRES 7 A 411 MET PRO ALA THR PRO THR PRO MET MET ILE LEU MET ASP SEQRES 8 A 411 PRO PRO ASP HIS THR ARG LEU ARG LYS LEU VAL GLY ARG SEQRES 9 A 411 SER PHE ALA VAL ARG ARG MET ASN GLU LEU GLU PRO ARG SEQRES 10 A 411 ILE THR GLU ILE ALA ASP GLY LEU LEU ALA GLY LEU PRO SEQRES 11 A 411 THR ASP GLY PRO VAL ASP LEU MET ARG GLU TYR ALA PHE SEQRES 12 A 411 GLN ILE PRO VAL GLN VAL ILE CYS GLU LEU LEU GLY VAL SEQRES 13 A 411 PRO ALA GLU ASP ARG ASP ASP PHE SER ALA TRP SER SER SEQRES 14 A 411 VAL LEU VAL ASP ASP SER PRO ALA ASP ASP LYS ASN ALA SEQRES 15 A 411 ALA MET GLY LYS LEU HIS GLY TYR LEU SER ASP LEU LEU SEQRES 16 A 411 GLU ARG LYS ARG THR GLU PRO ASP ASP ALA LEU LEU SER SEQRES 17 A 411 SER LEU LEU ALA VAL SER ASP GLU ASP GLY ASP ARG LEU SEQRES 18 A 411 SER GLN GLU GLU LEU VAL ALA MET ALA MET LEU LEU LEU SEQRES 19 A 411 ILE ALA GLY HIS GLU THR THR VAL ASN LEU ILE GLY ASN SEQRES 20 A 411 GLY VAL LEU ALA LEU LEU THR HIS PRO ASP GLN ARG LYS SEQRES 21 A 411 LEU LEU ALA GLU ASP PRO SER LEU ILE SER SER ALA VAL SEQRES 22 A 411 GLU GLU PHE LEU ARG PHE ASP SER PRO VAL SER GLN ALA SEQRES 23 A 411 PRO ILE ARG PHE THR ALA GLU ASP VAL THR TYR SER GLY SEQRES 24 A 411 VAL THR ILE PRO ALA GLY GLU MET VAL MET LEU GLY LEU SEQRES 25 A 411 ALA ALA ALA ASN ARG ASP ALA ASP TRP MET PRO GLU PRO SEQRES 26 A 411 ASP ARG LEU ASP ILE THR ARG ASP ALA SER GLY GLY VAL SEQRES 27 A 411 PHE PHE GLY HIS GLY ILE HIS PHE CYS LEU GLY ALA GLN SEQRES 28 A 411 LEU ALA ARG LEU GLU GLY ARG VAL ALA ILE GLY ARG LEU SEQRES 29 A 411 PHE ALA ASP ARG PRO GLU LEU ALA LEU ALA VAL GLY LEU SEQRES 30 A 411 ASP GLU LEU VAL TYR ARG GLU SER THR LEU VAL ARG GLY SEQRES 31 A 411 LEU SER ARG MET PRO VAL THR MET GLY PRO ARG SER ALA SEQRES 32 A 411 LEU GLU HIS HIS HIS HIS HIS HIS HET HEM A 501 43 HET VD3 A 502 56 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM VD3 (1S,3Z)-3-[(2E)-2-[(1R,3AR,7AS)-7A-METHYL-1-[(2R)-6- HETNAM 2 VD3 METHYLHEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4- HETNAM 3 VD3 YLIDENE]ETHYLI DENE]-4-METHYLIDENE-CYCLOHEXAN-1-OL HETSYN HEM HEME HETSYN VD3 VITAMIN D3 FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 VD3 C27 H44 O FORMUL 4 HOH *36(H2 O) HELIX 1 1 SER A 15 GLN A 20 5 6 HELIX 2 2 PRO A 22 ASP A 33 1 12 HELIX 3 3 ARG A 50 VAL A 59 1 10 HELIX 4 4 ASP A 66 THR A 70 5 5 HELIX 5 5 PRO A 72 ARG A 76 5 5 HELIX 6 6 MET A 86 MET A 90 5 5 HELIX 7 7 PRO A 93 ARG A 104 1 12 HELIX 8 8 ALA A 107 GLU A 113 1 7 HELIX 9 9 LEU A 114 ALA A 127 1 14 HELIX 10 10 LEU A 137 TYR A 141 1 5 HELIX 11 11 PHE A 143 GLY A 155 1 13 HELIX 12 12 PRO A 157 GLU A 159 5 3 HELIX 13 13 ASP A 160 ASP A 173 1 14 HELIX 14 14 PRO A 176 GLU A 201 1 26 HELIX 15 15 ALA A 205 ASP A 217 1 13 HELIX 16 16 SER A 222 HIS A 255 1 34 HELIX 17 17 HIS A 255 ASP A 265 1 11 HELIX 18 18 LEU A 268 ASP A 280 1 13 HELIX 19 19 GLY A 311 ASN A 316 1 6 HELIX 20 20 GLY A 349 ARG A 368 1 20 HELIX 21 21 GLY A 376 LEU A 380 5 5 SHEET 1 A 5 VAL A 35 LEU A 40 0 SHEET 2 A 5 GLY A 43 LEU A 48 -1 O LEU A 47 N ARG A 36 SHEET 3 A 5 MET A 307 LEU A 310 1 O MET A 309 N TRP A 46 SHEET 4 A 5 ARG A 289 THR A 291 -1 N ARG A 289 O VAL A 308 SHEET 5 A 5 LEU A 63 SER A 64 -1 N SER A 64 O PHE A 290 SHEET 1 B 3 PRO A 134 ASP A 136 0 SHEET 2 B 3 PRO A 395 THR A 397 -1 O VAL A 396 N VAL A 135 SHEET 3 B 3 ALA A 372 LEU A 373 -1 N ALA A 372 O THR A 397 SHEET 1 C 2 VAL A 295 TYR A 297 0 SHEET 2 C 2 VAL A 300 ILE A 302 -1 O VAL A 300 N TYR A 297 LINK SG CYS A 347 FE HEM A 501 1555 1555 2.38 CISPEP 1 PRO A 92 PRO A 93 0 -0.26 SITE 1 AC1 24 PHE A 58 LYS A 65 MET A 87 ILE A 88 SITE 2 AC1 24 HIS A 95 ARG A 99 LEU A 232 ALA A 236 SITE 3 AC1 24 THR A 240 THR A 241 PRO A 282 VAL A 283 SITE 4 AC1 24 ALA A 286 PRO A 287 ARG A 289 LEU A 312 SITE 5 AC1 24 PHE A 339 PHE A 340 GLY A 341 HIS A 345 SITE 6 AC1 24 CYS A 347 GLY A 349 VD3 A 502 HOH A 620 SITE 1 AC2 3 ILE A 235 ALA A 236 HEM A 501 CRYST1 61.421 105.521 141.988 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 0.016281 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009477 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007043 0.00000