HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 28-SEP-15 5E0E TITLE CRYSTAL STRUCTURE OF CYTOCHROME P450 2B37 FROM DESERT WOODRAT IN TITLE 2 COMPLEX WITH 4-(4-CHLOROPHENYL)IMIDAZOLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450 FAMILY 2 SUBFAMILY B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 29-491; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEOTOMA LEPIDA; SOURCE 3 ORGANISM_COMMON: DESERT WOODRAT; SOURCE 4 ORGANISM_TAXID: 56216; SOURCE 5 GENE: CYP2B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C43 (DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PKK KEYWDS CYTOCHROME P450, CYP2B37, 4-(4-CHLOROPHENYL)IMIDAZOLE, INHIBITOR, KEYWDS 2 OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.B.SHAH,J.R.HALPERT,C.D.STOUT REVDAT 5 27-SEP-23 5E0E 1 REMARK REVDAT 4 27-NOV-19 5E0E 1 REMARK REVDAT 3 13-SEP-17 5E0E 1 JRNL REMARK REVDAT 2 23-MAR-16 5E0E 1 JRNL REVDAT 1 10-FEB-16 5E0E 0 JRNL AUTH M.B.SHAH,J.LIU,L.HUO,Q.ZHANG,M.D.DEARING,P.R.WILDERMAN, JRNL AUTH 2 G.D.SZKLARZ,C.D.STOUT,J.R.HALPERT JRNL TITL STRUCTURE-FUNCTION ANALYSIS OF MAMMALIAN CYP2B ENZYMES USING JRNL TITL 2 7-SUBSTITUTED COUMARIN DERIVATIVES AS PROBES: UTILITY OF JRNL TITL 3 CRYSTAL STRUCTURES AND MOLECULAR MODELING IN UNDERSTANDING JRNL TITL 4 XENOBIOTIC METABOLISM. JRNL REF MOL.PHARMACOL. V. 89 435 2016 JRNL REFN ESSN 1521-0111 JRNL PMID 26826176 JRNL DOI 10.1124/MOL.115.102111 REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 3.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 13863 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 756 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) : 3.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 949 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.3450 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.3650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3589 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 79 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 86.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : -0.24000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.523 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.396 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 24.990 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.887 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3794 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5170 ; 1.839 ; 2.009 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 462 ; 8.337 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;38.608 ;23.491 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 568 ;23.878 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;22.384 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 558 ; 0.119 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2954 ; 0.008 ; 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): 2312 ; 0.713 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3718 ; 1.369 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1482 ; 1.599 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1452 ; 2.880 ; 4.500 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5E0E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213880. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14619 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.400 REMARK 200 RESOLUTION RANGE LOW (A) : 42.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1SUO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS AND 45% POLYPROPYLENE REMARK 280 GLYCOL P400, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 72.38500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 72.38500 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.23500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 72.38500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.11750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 72.38500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 78.35250 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 72.38500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 72.38500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 52.23500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 72.38500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 78.35250 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 72.38500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 26.11750 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: 2540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 30 CG CD1 CD2 REMARK 470 ARG A 35 CZ NH1 NH2 REMARK 470 ARG A 48 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 51 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 56 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 57 NE CZ NH1 NH2 REMARK 470 ARG A 109 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 126 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 129 CD1 CD2 REMARK 470 MET A 137 CG SD CE REMARK 470 LYS A 139 CG CD CE NZ REMARK 470 ARG A 140 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 151 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 155 CG CD OE1 OE2 REMARK 470 ARG A 158 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 191 CG CD CE NZ REMARK 470 ARG A 197 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 225 CD CE NZ REMARK 470 LYS A 276 CD CE NZ REMARK 470 GLN A 279 CG CD OE1 NE2 REMARK 470 LYS A 323 CG CD CE NZ REMARK 470 LYS A 326 CG CD CE NZ REMARK 470 HIS A 335 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 336 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 345 CG CD CE NZ REMARK 470 ARG A 358 CG CD NE CZ NH1 NH2 REMARK 470 SER A 360 OG REMARK 470 LYS A 384 CG CD CE NZ REMARK 470 GLU A 387 OE1 OE2 REMARK 470 GLN A 404 CG CD OE1 NE2 REMARK 470 ASP A 411 CG OD1 OD2 REMARK 470 LYS A 421 CG CD CE NZ REMARK 470 ILE A 431 CD1 REMARK 470 LEU A 459 CG CD1 CD2 REMARK 470 SER A 460 OG REMARK 470 SER A 461 OG REMARK 470 VAL A 463 CG1 CG2 REMARK 470 LYS A 466 CG CD CE NZ REMARK 470 SER A 475 OG REMARK 470 PHE A 477 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 479 CE NZ REMARK 470 GLN A 482 CG CD OE1 NE2 REMARK 470 LEU A 489 CG CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 FE HEM A 501 N1 CPZ A 502 1.63 REMARK 500 O ILE A 391 OG SER A 394 1.67 REMARK 500 O LEU A 392 N ALA A 395 2.03 REMARK 500 O LEU A 44 OD2 ASP A 47 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 31 CB - CA - C ANGL. DEV. = -15.7 DEGREES REMARK 500 MET A 46 O - C - N ANGL. DEV. = 14.1 DEGREES REMARK 500 LYS A 61 CB - CA - C ANGL. DEV. = -13.6 DEGREES REMARK 500 LYS A 61 N - CA - C ANGL. DEV. = 18.8 DEGREES REMARK 500 VAL A 114 CB - CA - C ANGL. DEV. = 16.0 DEGREES REMARK 500 VAL A 114 N - CA - C ANGL. DEV. = -25.6 DEGREES REMARK 500 SER A 141 N - CA - CB ANGL. DEV. = 24.2 DEGREES REMARK 500 SER A 141 CA - CB - OG ANGL. DEV. = 34.6 DEGREES REMARK 500 SER A 141 N - CA - C ANGL. DEV. = -23.6 DEGREES REMARK 500 GLN A 161 CB - CA - C ANGL. DEV. = -12.9 DEGREES REMARK 500 GLN A 161 N - CA - C ANGL. DEV. = 25.8 DEGREES REMARK 500 GLU A 240 O - C - N ANGL. DEV. = 10.3 DEGREES REMARK 500 GLN A 404 N - CA - C ANGL. DEV. = -19.7 DEGREES REMARK 500 ASN A 456 CA - C - O ANGL. DEV. = -13.5 DEGREES REMARK 500 PHE A 457 CB - CA - C ANGL. DEV. = -16.9 DEGREES REMARK 500 PHE A 457 N - CA - CB ANGL. DEV. = 23.4 DEGREES 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 GLN A 45 0.60 -54.97 REMARK 500 ASP A 47 -38.24 -37.85 REMARK 500 ARG A 48 107.62 -48.38 REMARK 500 LEU A 52 -33.36 -140.05 REMARK 500 GLU A 60 108.54 -34.01 REMARK 500 ILE A 107 -71.56 -89.82 REMARK 500 ARG A 109 37.77 37.33 REMARK 500 VAL A 114 -58.81 -141.30 REMARK 500 ASN A 117 -162.24 -112.89 REMARK 500 ARG A 133 -57.67 68.47 REMARK 500 ASP A 134 38.25 -94.35 REMARK 500 ARG A 140 -90.68 -115.64 REMARK 500 ASP A 166 104.27 -57.25 REMARK 500 LEU A 198 -41.14 -139.44 REMARK 500 SER A 210 54.02 -99.80 REMARK 500 PRO A 228 -178.98 -65.79 REMARK 500 ASP A 263 -163.96 -168.91 REMARK 500 HIS A 280 19.96 -151.61 REMARK 500 PHE A 283 61.03 -102.67 REMARK 500 THR A 300 -82.66 -117.33 REMARK 500 ILE A 332 -73.44 -123.13 REMARK 500 HIS A 335 -63.69 -97.37 REMARK 500 ARG A 336 171.59 -55.22 REMARK 500 GLU A 341 71.59 -68.02 REMARK 500 ASP A 342 -65.94 -142.42 REMARK 500 ARG A 343 -33.89 -35.22 REMARK 500 ASP A 361 66.18 31.95 REMARK 500 PRO A 368 119.38 -34.59 REMARK 500 ASP A 374 153.69 -48.80 REMARK 500 GLN A 404 76.27 -106.42 REMARK 500 ASN A 409 89.69 -170.31 REMARK 500 ASP A 411 3.53 -60.15 REMARK 500 ASN A 417 26.23 -78.69 REMARK 500 GLU A 424 -5.13 -59.52 REMARK 500 SER A 430 -171.25 80.49 REMARK 500 CYS A 436 122.80 -31.94 REMARK 500 ILE A 453 -71.89 -68.07 REMARK 500 LEU A 454 -9.94 -54.39 REMARK 500 PHE A 457 122.66 -172.41 REMARK 500 SER A 475 -60.58 -106.62 REMARK 500 LYS A 479 137.12 -34.10 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 VAL A 114 PHE A 115 -144.08 REMARK 500 LYS A 139 ARG A 140 35.05 REMARK 500 ASN A 456 PHE A 457 -135.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 125 0.17 SIDE CHAIN REMARK 500 ARG A 187 0.17 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 MET A 46 10.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 616 DISTANCE = 7.59 ANGSTROMS 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 436 SG REMARK 620 2 HEM A 501 NA 93.9 REMARK 620 3 HEM A 501 NB 90.9 93.4 REMARK 620 4 HEM A 501 NC 93.9 172.0 88.0 REMARK 620 5 HEM A 501 ND 95.1 83.8 173.5 94.0 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 CPZ A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CPZ A 504 DBREF 5E0E A 29 491 UNP J9JD75 J9JD75_NEOLE 29 491 SEQRES 1 A 463 HIS LEU PRO PRO GLY PRO ARG PRO LEU PRO LEU LEU GLY SEQRES 2 A 463 ASN LEU LEU GLN MET ASP ARG GLY GLY PHE LEU ASN SER SEQRES 3 A 463 PHE ARG ARG ILE ARG GLU LYS TYR GLY ASP VAL PHE THR SEQRES 4 A 463 VAL HIS LEU GLY PRO ARG PRO VAL VAL MET LEU TYR GLY SEQRES 5 A 463 THR GLU ALA ILE ARG GLU ALA LEU VAL ASP GLN ALA GLU SEQRES 6 A 463 ALA PHE SER GLY ARG GLY THR ILE ALA VAL VAL GLU PRO SEQRES 7 A 463 ILE PHE ARG GLY TYR GLY VAL VAL PHE ALA ASN GLY GLU SEQRES 8 A 463 ARG TRP LYS ALA LEU ARG ARG PHE SER LEU VAL THR MET SEQRES 9 A 463 ARG ASP PHE GLY MET GLY LYS ARG SER VAL GLU GLU ARG SEQRES 10 A 463 ILE GLN GLU GLU ALA ARG CYS LEU VAL GLU GLU PHE ARG SEQRES 11 A 463 LYS SER GLN GLY ALA PRO LEU ASP PRO THR PHE LEU PHE SEQRES 12 A 463 GLN CYS ILE THR ALA ASN ILE ILE CYS SER ILE VAL PHE SEQRES 13 A 463 GLY GLU ARG PHE ASP TYR LYS ASP HIS GLN PHE LEU ARG SEQRES 14 A 463 LEU LEU TYR LEU PHE TYR GLN SER PHE SER LEU ILE SER SEQRES 15 A 463 SER PHE SER SER GLN VAL PHE GLU LEU PHE SER GLY PHE SEQRES 16 A 463 LEU LYS TYR PHE PRO GLY THR HIS ARG GLN ILE SER ARG SEQRES 17 A 463 ASN LEU GLN GLU ILE LEU ASP TYR ILE GLY GLN SER VAL SEQRES 18 A 463 GLU LYS HIS ARG ALA THR LEU ASP PRO SER HIS PRO ARG SEQRES 19 A 463 ASP PHE ILE ASP THR TYR LEU LEU ARG MET GLU LYS GLU SEQRES 20 A 463 LYS SER ASN GLN HIS THR GLU PHE ASP HIS GLN ASN LEU SEQRES 21 A 463 VAL ILE SER VAL LEU SER LEU PHE PHE ALA GLY THR GLU SEQRES 22 A 463 THR SER SER THR THR LEU ARG TYR GLY PHE LEU LEU MET SEQRES 23 A 463 LEU LYS TYR PRO HIS VAL ALA GLU LYS VAL GLN LYS GLU SEQRES 24 A 463 ILE ASP GLN VAL ILE GLY SER HIS ARG LEU PRO THR LEU SEQRES 25 A 463 GLU ASP ARG THR LYS MET PRO TYR THR GLU ALA VAL ILE SEQRES 26 A 463 TYR GLU ILE GLN ARG PHE SER ASP LEU ILE PRO ILE GLY SEQRES 27 A 463 VAL PRO HIS LYS VAL THR LYS ASP THR LEU PHE ARG GLY SEQRES 28 A 463 TYR LEU LEU PRO LYS ASN THR GLU VAL TYR PRO ILE LEU SEQRES 29 A 463 SER SER ALA LEU HIS ASP PRO GLN TYR PHE GLU GLN PRO SEQRES 30 A 463 ASP THR PHE ASN PRO ASP HIS PHE LEU ASP ALA ASN GLY SEQRES 31 A 463 ALA LEU LYS LYS SER GLU ALA PHE MET PRO PHE SER ILE SEQRES 32 A 463 GLY LYS ARG ILE CYS LEU GLY GLU GLY ILE ALA ARG ASN SEQRES 33 A 463 GLU LEU PHE LEU PHE PHE THR THR ILE LEU GLN ASN PHE SEQRES 34 A 463 SER LEU SER SER PRO VAL ALA PRO LYS ASP ILE ASP LEU SEQRES 35 A 463 SER PRO LYS GLU SER GLY PHE GLY LYS VAL PRO GLN THR SEQRES 36 A 463 TYR GLN ILE CYS PHE LEU ALA ARG HET HEM A 501 43 HET CPZ A 502 12 HET CPZ A 503 12 HET CPZ A 504 12 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CPZ 4-(4-CHLOROPHENYL)IMIDAZOLE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 CPZ 3(C9 H7 CL N2) FORMUL 6 HOH *16(H2 O) HELIX 1 AA1 LEU A 52 ARG A 59 1 8 HELIX 2 AA2 GLY A 80 VAL A 89 1 10 HELIX 3 AA3 GLN A 91 SER A 96 1 6 HELIX 4 AA4 VAL A 104 ARG A 109 1 6 HELIX 5 AA5 ASN A 117 THR A 131 1 15 HELIX 6 AA6 SER A 141 LYS A 159 1 19 HELIX 7 AA7 PRO A 167 GLY A 185 1 19 HELIX 8 AA8 ASP A 192 TYR A 200 1 9 HELIX 9 AA9 PHE A 202 SER A 210 1 9 HELIX 10 AB1 SER A 211 LYS A 225 1 15 HELIX 11 AB2 GLY A 229 LEU A 256 1 28 HELIX 12 AB3 ASP A 263 GLU A 275 1 13 HELIX 13 AB4 LYS A 276 ASN A 278 5 3 HELIX 14 AB5 ASP A 284 THR A 300 1 17 HELIX 15 AB6 THR A 300 TYR A 317 1 18 HELIX 16 AB7 HIS A 319 ILE A 332 1 14 HELIX 17 AB8 ASP A 342 LYS A 345 5 4 HELIX 18 AB9 MET A 346 ASP A 361 1 16 HELIX 19 AC1 LEU A 392 HIS A 397 1 6 HELIX 20 AC2 ASN A 409 PHE A 413 5 5 HELIX 21 AC3 GLY A 438 ASN A 456 1 19 HELIX 22 AC4 ALA A 464 ILE A 468 5 5 SHEET 1 AA1 5 VAL A 65 LEU A 70 0 SHEET 2 AA1 5 ARG A 73 TYR A 79 -1 O ARG A 73 N LEU A 70 SHEET 3 AA1 5 GLU A 387 ILE A 391 1 O ILE A 391 N LEU A 78 SHEET 4 AA1 5 HIS A 369 LYS A 370 -1 N HIS A 369 O VAL A 388 SHEET 5 AA1 5 GLY A 97 ARG A 98 -1 N GLY A 97 O LYS A 370 SHEET 1 AA2 2 THR A 375 PHE A 377 0 SHEET 2 AA2 2 TYR A 380 LEU A 382 -1 O TYR A 380 N PHE A 377 SHEET 1 AA3 2 PHE A 457 SER A 460 0 SHEET 2 AA3 2 CYS A 487 ALA A 490 -1 O LEU A 489 N SER A 458 LINK C TYR A 200 CA LEU A 201 1555 1555 1.45 LINK SG CYS A 436 FE HEM A 501 1555 1555 1.95 CISPEP 1 GLU A 60 LYS A 61 0 17.84 CISPEP 2 MET A 137 GLY A 138 0 1.93 CISPEP 3 GLY A 138 LYS A 139 0 0.03 SITE 1 AC1 22 ARG A 98 VAL A 113 VAL A 114 TRP A 121 SITE 2 AC1 22 ARG A 125 ILE A 179 ALA A 298 GLY A 299 SITE 3 AC1 22 THR A 302 GLN A 357 ILE A 363 VAL A 367 SITE 4 AC1 22 HIS A 369 PRO A 428 PHE A 429 SER A 430 SITE 5 AC1 22 ARG A 434 CYS A 436 LEU A 437 GLY A 438 SITE 6 AC1 22 ILE A 441 CPZ A 502 SITE 1 AC2 6 ILE A 101 ALA A 298 THR A 302 VAL A 367 SITE 2 AC2 6 CYS A 436 HEM A 501 SITE 1 AC3 2 ASP A 47 GLN A 215 CRYST1 144.770 144.770 104.470 90.00 90.00 90.00 I 41 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 0.006908 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006908 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009572 0.00000