HEADER OXIDOREDUCTASE 22-JUL-16 5GNL TITLE CYTOCHROME P450 VDH (CYP107BR1) F106V MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN D(3) 25-HYDROXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOCHROME P450, CYP107BR1; COMPND 5 EC: 1.14.15.15; 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 GENE: VDH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 CODONPLUS (DE3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET29B KEYWDS OXIDOREDUCTASE, CYTOCHROME P450 EXPDTA X-RAY DIFFRACTION AUTHOR Y.YASUTAKE,T.TAMURA REVDAT 2 08-NOV-23 5GNL 1 REMARK REVDAT 1 17-MAY-17 5GNL 0 JRNL AUTH Y.YASUTAKE,T.KAMEDA,T.TAMURA JRNL TITL STRUCTURAL INSIGHTS INTO THE MECHANISM OF THE DRASTIC JRNL TITL 2 CHANGES IN ENZYMATIC ACTIVITY OF THE CYTOCHROME P450 VITAMIN JRNL TITL 3 D3 HYDROXYLASE (CYP107BR1) CAUSED BY A MUTATION DISTANT FROM JRNL TITL 4 THE ACTIVE SITE JRNL REF ACTA CRYSTALLOGR F STRUCT V. 73 266 2017 JRNL REF 2 BIOL COMMUN JRNL REFN ESSN 2053-230X JRNL PMID 28471358 JRNL DOI 10.1107/S2053230X17004782 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 28831 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1522 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2133 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE SET COUNT : 125 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3058 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 117 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.89000 REMARK 3 B22 (A**2) : 0.89000 REMARK 3 B33 (A**2) : -2.88000 REMARK 3 B12 (A**2) : 0.44000 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): 0.178 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.156 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.124 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.122 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3180 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4337 ; 1.536 ; 2.006 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 394 ; 6.280 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 142 ;35.709 ;23.239 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 514 ;16.344 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;18.879 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 484 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2438 ; 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): 1579 ; 0.851 ; 2.225 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1972 ; 1.463 ; 3.333 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1601 ; 0.985 ; 2.335 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): 4944 ; 5.270 ;19.245 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 : 3 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 9 A 83 REMARK 3 ORIGIN FOR THE GROUP (A): 2.4203 -4.7200 -7.7898 REMARK 3 T TENSOR REMARK 3 T11: 0.2716 T22: 0.0759 REMARK 3 T33: 0.1460 T12: -0.0014 REMARK 3 T13: 0.1064 T23: -0.0158 REMARK 3 L TENSOR REMARK 3 L11: 3.9173 L22: 3.5589 REMARK 3 L33: 4.9606 L12: -2.2420 REMARK 3 L13: 1.6366 L23: -0.9524 REMARK 3 S TENSOR REMARK 3 S11: 0.1683 S12: 0.3699 S13: 0.1111 REMARK 3 S21: -0.6756 S22: -0.1432 S23: -0.3599 REMARK 3 S31: 0.1550 S32: 0.5554 S33: -0.0252 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 84 A 184 REMARK 3 ORIGIN FOR THE GROUP (A): 2.6533 20.4944 1.6397 REMARK 3 T TENSOR REMARK 3 T11: 0.6780 T22: 0.1457 REMARK 3 T33: 0.2930 T12: -0.1658 REMARK 3 T13: -0.0461 T23: -0.0122 REMARK 3 L TENSOR REMARK 3 L11: 5.1165 L22: 3.3802 REMARK 3 L33: 2.1200 L12: -2.9809 REMARK 3 L13: 2.6112 L23: -1.7919 REMARK 3 S TENSOR REMARK 3 S11: 0.1227 S12: 0.5160 S13: 0.3849 REMARK 3 S21: -0.3392 S22: -0.4020 S23: -0.3219 REMARK 3 S31: -0.5807 S32: 0.5003 S33: 0.2793 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 185 A 403 REMARK 3 ORIGIN FOR THE GROUP (A): -3.8901 11.0606 1.7231 REMARK 3 T TENSOR REMARK 3 T11: 0.1683 T22: 0.0187 REMARK 3 T33: 0.1041 T12: -0.0018 REMARK 3 T13: 0.0173 T23: -0.0278 REMARK 3 L TENSOR REMARK 3 L11: 1.3967 L22: 2.7876 REMARK 3 L33: 2.0656 L12: -0.7198 REMARK 3 L13: 0.4994 L23: -0.3716 REMARK 3 S TENSOR REMARK 3 S11: -0.0615 S12: -0.1340 S13: 0.1060 REMARK 3 S21: -0.1450 S22: -0.0154 S23: 0.0587 REMARK 3 S31: -0.3559 S32: -0.0414 S33: 0.0769 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5GNL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1300000977. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30377 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 46.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : 0.94900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3A4G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, 25-75 MM NACL, 50 MM REMARK 280 CACL2, 38-42% PEG400, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.72200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 65.44400 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 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 ALA A 2 REMARK 465 LEU A 3 REMARK 465 THR A 4 REMARK 465 THR A 5 REMARK 465 THR A 6 REMARK 465 GLY A 7 REMARK 465 THR A 8 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 GLN A 10 98.97 -66.83 REMARK 500 ALA A 77 2.83 -57.71 REMARK 500 PRO A 85 39.84 -60.84 REMARK 500 TYR A 141 -67.68 -133.22 REMARK 500 ASP A 173 110.81 -6.62 REMARK 500 ASP A 174 -65.59 -130.43 REMARK 500 ALA A 177 47.76 -76.56 REMARK 500 ASP A 215 -175.42 -67.18 REMARK 500 HIS A 238 -74.46 -89.02 REMARK 500 ASP A 280 69.03 -156.68 REMARK 500 HIS A 342 138.63 -172.08 REMARK 500 CYS A 347 116.30 -39.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 334 SER A 335 -148.23 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 97.7 REMARK 620 3 HEM A 501 NB 83.7 89.7 REMARK 620 4 HEM A 501 NC 83.8 178.2 89.3 REMARK 620 5 HEM A 501 ND 97.6 90.4 178.6 90.5 REMARK 620 6 HOH A 665 O 173.3 80.9 89.7 97.5 88.9 REMARK 620 N 1 2 3 4 5 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 PG0 A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GNM RELATED DB: PDB DBREF 5GNL A 1 403 UNP C4B644 CPVDH_PSEAH 1 403 SEQADV 5GNL VAL A 106 UNP C4B644 PHE 106 ENGINEERED MUTATION SEQADV 5GNL LEU A 404 UNP C4B644 EXPRESSION TAG SEQADV 5GNL GLU A 405 UNP C4B644 EXPRESSION TAG SEQADV 5GNL HIS A 406 UNP C4B644 EXPRESSION TAG SEQADV 5GNL HIS A 407 UNP C4B644 EXPRESSION TAG SEQADV 5GNL HIS A 408 UNP C4B644 EXPRESSION TAG SEQADV 5GNL HIS A 409 UNP C4B644 EXPRESSION TAG SEQADV 5GNL HIS A 410 UNP C4B644 EXPRESSION TAG SEQADV 5GNL 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 VAL THR 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 PG0 A 502 8 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM PG0 2-(2-METHOXYETHOXY)ETHANOL HETSYN HEM HEME HETSYN PG0 PEG 6000 FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 PG0 C5 H12 O3 FORMUL 4 HOH *117(H2 O) HELIX 1 AA1 SER A 15 TRP A 19 5 5 HELIX 2 AA2 PRO A 22 ASP A 33 1 12 HELIX 3 AA3 ARG A 50 VAL A 59 1 10 HELIX 4 AA4 ASP A 66 LEU A 71 5 6 HELIX 5 AA5 PRO A 72 ARG A 76 5 5 HELIX 6 AA6 MET A 86 MET A 90 5 5 HELIX 7 AA7 PRO A 93 ARG A 104 1 12 HELIX 8 AA8 THR A 107 LEU A 114 1 8 HELIX 9 AA9 LEU A 114 GLY A 128 1 15 HELIX 10 AB1 LEU A 137 TYR A 141 1 5 HELIX 11 AB2 PHE A 143 GLY A 155 1 13 HELIX 12 AB3 PRO A 157 GLU A 159 5 3 HELIX 13 AB4 ASP A 160 VAL A 172 1 13 HELIX 14 AB5 ASP A 179 GLU A 201 1 23 HELIX 15 AB6 ALA A 205 VAL A 213 1 9 HELIX 16 AB7 SER A 222 HIS A 238 1 17 HELIX 17 AB8 HIS A 238 THR A 254 1 17 HELIX 18 AB9 HIS A 255 ASP A 265 1 11 HELIX 19 AC1 LEU A 268 ASP A 280 1 13 HELIX 20 AC2 GLY A 311 ASN A 316 1 6 HELIX 21 AC3 GLY A 349 ARG A 368 1 20 HELIX 22 AC4 GLY A 376 LEU A 380 5 5 SHEET 1 AA1 5 VAL A 35 LEU A 38 0 SHEET 2 AA1 5 VAL A 45 LEU A 48 -1 O VAL A 45 N LEU A 38 SHEET 3 AA1 5 MET A 307 LEU A 310 1 O MET A 309 N TRP A 46 SHEET 4 AA1 5 ARG A 289 THR A 291 -1 N ARG A 289 O VAL A 308 SHEET 5 AA1 5 LEU A 63 SER A 64 -1 N SER A 64 O PHE A 290 SHEET 1 AA2 3 VAL A 135 ASP A 136 0 SHEET 2 AA2 3 PRO A 395 THR A 397 -1 O VAL A 396 N VAL A 135 SHEET 3 AA2 3 ALA A 372 LEU A 373 -1 N ALA A 372 O THR A 397 SHEET 1 AA3 2 VAL A 295 TYR A 297 0 SHEET 2 AA3 2 VAL A 300 ILE A 302 -1 O ILE A 302 N VAL A 295 LINK SG CYS A 347 FE HEM A 501 1555 1555 2.45 LINK FE HEM A 501 O HOH A 665 1555 1555 2.41 CISPEP 1 PRO A 92 PRO A 93 0 6.89 CISPEP 2 GLY A 133 PRO A 134 0 -3.57 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 ALA A 236 GLY A 237 SITE 3 AC1 24 THR A 240 THR A 241 LEU A 244 PRO A 287 SITE 4 AC1 24 ARG A 289 PHE A 339 PHE A 340 GLY A 341 SITE 5 AC1 24 ILE A 344 HIS A 345 CYS A 347 LEU A 348 SITE 6 AC1 24 GLY A 349 ALA A 353 HOH A 635 HOH A 665 SITE 1 AC2 3 ILE A 88 PRO A 287 HOH A 665 CRYST1 61.670 61.670 98.166 90.00 90.00 120.00 P 31 3 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 0.016215 0.009362 0.000000 0.00000 SCALE2 0.000000 0.018724 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010187 0.00000