HEADER OXIDOREDUCTASE 17-APR-12 4EP6 TITLE CRYSTAL STRUCTURE OF THE XPLA HEME DOMAIN IN COMPLEX WITH IMIDAZOLE TITLE 2 AND PEG COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450-LIKE PROTEIN XPLA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HEME DOMAIN (UNP RESIDUES 161-552); COMPND 5 EC: 1.-.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOCOCCUS RHODOCHROUS; SOURCE 3 ORGANISM_TAXID: 1829; SOURCE 4 GENE: XPLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS P450 ENZYME, P450 MONOXYGENASE, EXPLOSIVE RDX, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.H.BUI,K.J.MCLEAN,M.R.CHEESMAN,J.M.BRADLEY,S.E.J.RIGBY,D.LEYS, AUTHOR 2 A.W.MUNRO REVDAT 3 13-SEP-23 4EP6 1 REMARK LINK REVDAT 2 20-JUN-12 4EP6 1 JRNL REVDAT 1 09-MAY-12 4EP6 0 JRNL AUTH S.H.BUI,K.J.MCLEAN,M.R.CHEESMAN,J.M.BRADLEY,S.E.RIGBY, JRNL AUTH 2 C.W.LEVY,D.LEYS,A.W.MUNRO JRNL TITL UNUSUAL SPECTROSCOPIC AND LIGAND BINDING PROPERTIES OF THE JRNL TITL 2 CYTOCHROME P450-FLAVODOXIN FUSION ENZYME XPLA. JRNL REF J.BIOL.CHEM. V. 287 19699 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22500029 JRNL DOI 10.1074/JBC.M111.319202 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 28983 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1534 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2142 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE SET COUNT : 103 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3056 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.45000 REMARK 3 B22 (A**2) : -3.45000 REMARK 3 B33 (A**2) : 6.89000 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): 0.212 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.190 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.154 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.152 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3189 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2145 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4358 ; 1.885 ; 2.004 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5177 ; 1.077 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 393 ; 6.827 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 150 ;31.690 ;23.200 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 475 ;15.192 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;16.789 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 472 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3597 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 661 ; 0.001 ; 0.020 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): 1967 ; 0.914 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 780 ; 0.213 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3169 ; 1.716 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1222 ; 2.884 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1188 ; 4.588 ; 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 : 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 161 A 552 REMARK 3 ORIGIN FOR THE GROUP (A): 6.5260 19.5650 1.9860 REMARK 3 T TENSOR REMARK 3 T11: 0.0050 T22: 0.0172 REMARK 3 T33: 0.1173 T12: 0.0012 REMARK 3 T13: 0.0022 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 0.7424 L22: 1.2943 REMARK 3 L33: 0.3391 L12: -0.1036 REMARK 3 L13: 0.0641 L23: 0.1162 REMARK 3 S TENSOR REMARK 3 S11: 0.0096 S12: 0.0466 S13: 0.2053 REMARK 3 S21: -0.0710 S22: -0.0246 S23: -0.0865 REMARK 3 S31: 0.0165 S32: -0.0574 S33: 0.0150 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 4EP6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000071898. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-11 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28983 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 43.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2WIV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM MAGNESIUM CHLORIDE, 0.1 M REMARK 280 IMIDAZOLE/MES, PH 6.5, 30% PEG550 MME, PEG20000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K 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 68.06000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 68.06000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.56500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 68.06000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.78250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 68.06000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 56.34750 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 68.06000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 68.06000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 37.56500 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 68.06000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 56.34750 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 68.06000 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 18.78250 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 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 166 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 259 CG CD CE NZ REMARK 480 ARG A 356 CG CD NE CZ NH1 NH2 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 O HOH A 798 O HOH A 823 1.66 REMARK 500 O HOH A 830 O HOH A 836 2.00 REMARK 500 O TYR A 389 O HOH A 798 2.07 REMARK 500 REMARK 500 REMARK: NULL 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),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 166 CB ARG A 166 CG -0.278 REMARK 500 GLU A 167 CG GLU A 167 CD 0.114 REMARK 500 GLU A 270 CD GLU A 270 OE1 0.082 REMARK 500 VAL A 314 CB VAL A 314 CG2 0.164 REMARK 500 ARG A 356 CB ARG A 356 CG -0.378 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 LYS A 259 CA - CB - CG ANGL. DEV. = -13.7 DEGREES REMARK 500 ARG A 336 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 336 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 MET A 351 CG - SD - CE ANGL. DEV. = 10.7 DEGREES REMARK 500 PRO A 437 C - N - CA ANGL. DEV. = 12.3 DEGREES REMARK 500 PRO A 437 C - N - CD ANGL. DEV. = -12.8 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 HIS A 191 56.56 -142.28 REMARK 500 ASP A 226 70.00 -116.83 REMARK 500 ASP A 235 43.77 -86.56 REMARK 500 ALA A 292 -65.74 -104.46 REMARK 500 MET A 394 -76.83 -86.76 REMARK 500 ASP A 435 59.57 -146.36 REMARK 500 ALA A 458 128.03 -36.18 REMARK 500 ASN A 470 -7.06 -57.36 REMARK 500 ALA A 489 87.82 139.13 REMARK 500 ALA A 490 17.85 102.86 REMARK 500 SER A 491 33.04 -146.69 REMARK 500 ASN A 538 -169.70 -125.32 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 489 ALA A 490 -146.67 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 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 503 SG REMARK 620 2 HEM A 601 NA 95.0 REMARK 620 3 HEM A 601 NB 83.6 92.6 REMARK 620 4 HEM A 601 NC 86.1 177.4 85.2 REMARK 620 5 HEM A 601 ND 97.5 85.0 177.4 97.2 REMARK 620 6 IMD A 602 N1 168.2 96.6 93.6 82.2 85.9 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 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE A 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WIV RELATED DB: PDB REMARK 900 XPLA HEME DOMAIN IN DISTINCT CRYSTAL FORM, WITHOUT PEG PRESENT REMARK 900 RELATED ID: 2WIY RELATED DB: PDB REMARK 900 XPLA HEME DOMAIN IN DISTINCT CRYSTAL FORM, WITHOUT PEG PRESENT DBREF 4EP6 A 161 552 UNP Q8GPH7 Q8GPH7_RHORH 161 552 SEQRES 1 A 392 ALA ALA SER ILE ASP ARG GLU LEU VAL PRO TRP SER ASP SEQRES 2 A 392 PRO GLU PHE ARG ASN ASN PRO TYR PRO TRP TYR ARG ARG SEQRES 3 A 392 LEU GLN GLN ASP HIS PRO VAL HIS LYS LEU GLU ASP GLY SEQRES 4 A 392 THR TYR LEU VAL SER ARG TYR ALA ASP VAL SER HIS PHE SEQRES 5 A 392 ALA LYS LEU PRO ILE MET SER VAL GLU PRO GLY TRP ALA SEQRES 6 A 392 ASP ALA GLY PRO TRP ALA VAL ALA SER ASP THR ALA LEU SEQRES 7 A 392 GLY SER ASP PRO PRO HIS HIS THR VAL LEU ARG ARG GLN SEQRES 8 A 392 THR ASN LYS TRP PHE THR PRO LYS LEU VAL ASP GLY TRP SEQRES 9 A 392 VAL ARG THR THR ARG GLU LEU VAL GLY ASP LEU LEU ASP SEQRES 10 A 392 GLY VAL GLU ALA GLY GLN VAL ILE GLU ALA ARG ARG ASP SEQRES 11 A 392 LEU ALA VAL VAL PRO THR HIS VAL THR MET ALA ARG VAL SEQRES 12 A 392 LEU GLN LEU PRO GLU ASP ASP ALA ASP ALA VAL MET GLU SEQRES 13 A 392 ALA MET PHE GLU ALA MET LEU MET GLN SER ALA GLU PRO SEQRES 14 A 392 ALA ASP GLY ASP VAL ASP ARG ALA ALA VAL ALA PHE GLY SEQRES 15 A 392 TYR LEU SER ALA ARG VAL ALA GLU MET LEU GLU ASP LYS SEQRES 16 A 392 ARG VAL ASN PRO GLY ASP GLY LEU ALA ASP SER LEU LEU SEQRES 17 A 392 ASP ALA ALA ARG ALA GLY GLU ILE THR GLU SER GLU ALA SEQRES 18 A 392 ILE ALA THR ILE LEU VAL PHE TYR ALA VAL GLY HIS MET SEQRES 19 A 392 ALA ILE GLY TYR LEU ILE ALA SER GLY ILE GLU LEU PHE SEQRES 20 A 392 ALA ARG ARG PRO GLU VAL PHE THR ALA PHE ARG ASN ASP SEQRES 21 A 392 GLU SER ALA ARG ALA ALA ILE ILE ASN GLU MET VAL ARG SEQRES 22 A 392 MET ASP PRO PRO GLN LEU SER PHE LEU ARG PHE PRO THR SEQRES 23 A 392 GLU ASP VAL GLU ILE GLY GLY VAL LEU ILE GLU ALA GLY SEQRES 24 A 392 SER PRO ILE ARG PHE MET ILE GLY ALA ALA ASN ARG ASP SEQRES 25 A 392 PRO GLU VAL PHE ASP ASP PRO ASP VAL PHE ASP HIS THR SEQRES 26 A 392 ARG PRO PRO ALA ALA SER ARG ASN LEU SER PHE GLY LEU SEQRES 27 A 392 GLY PRO HIS SER CYS ALA GLY GLN ILE ILE SER ARG ALA SEQRES 28 A 392 GLU ALA THR THR VAL PHE ALA VAL LEU ALA GLU ARG TYR SEQRES 29 A 392 GLU ARG ILE GLU LEU ALA GLU GLU PRO THR VAL ALA HIS SEQRES 30 A 392 ASN ASP PHE ALA ARG ARG TYR ARG LYS LEU PRO ILE VAL SEQRES 31 A 392 LEU SER HET HEM A 601 43 HET IMD A 602 5 HET 1PE A 603 16 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM IMD IMIDAZOLE HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN HEM HEME HETSYN 1PE PEG400 FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 IMD C3 H5 N2 1+ FORMUL 4 1PE C10 H22 O6 FORMUL 5 HOH *147(H2 O) HELIX 1 1 ALA A 161 VAL A 169 1 9 HELIX 2 2 ASP A 173 ASN A 179 1 7 HELIX 3 3 PRO A 180 HIS A 191 1 12 HELIX 4 4 ARG A 205 ALA A 213 1 9 HELIX 5 5 VAL A 220 ALA A 225 5 6 HELIX 6 6 ALA A 227 SER A 234 5 8 HELIX 7 7 THR A 236 SER A 240 5 5 HELIX 8 8 PRO A 243 LYS A 254 1 12 HELIX 9 9 THR A 257 VAL A 265 1 9 HELIX 10 10 VAL A 265 GLY A 278 1 14 HELIX 11 11 ALA A 287 LEU A 291 1 5 HELIX 12 12 ALA A 292 GLN A 305 1 14 HELIX 13 13 ASP A 310 MET A 322 1 13 HELIX 14 14 LEU A 323 SER A 326 5 4 HELIX 15 15 GLY A 332 ASN A 358 1 27 HELIX 16 16 GLY A 362 ALA A 373 1 12 HELIX 17 17 THR A 377 GLY A 392 1 16 HELIX 18 18 MET A 394 ARG A 410 1 17 HELIX 19 19 ARG A 410 ASP A 420 1 11 HELIX 20 20 ALA A 423 ASP A 435 1 13 HELIX 21 21 MET A 465 ASN A 470 1 6 HELIX 22 22 LEU A 498 SER A 502 5 5 HELIX 23 23 GLY A 505 TYR A 524 1 20 SHEET 1 A 5 VAL A 193 LYS A 195 0 SHEET 2 A 5 TYR A 201 VAL A 203 -1 O LEU A 202 N HIS A 194 SHEET 3 A 5 ILE A 462 PHE A 464 1 O ARG A 463 N TYR A 201 SHEET 4 A 5 PHE A 441 PRO A 445 -1 N ARG A 443 O ILE A 462 SHEET 5 A 5 MET A 218 SER A 219 -1 N SER A 219 O PHE A 444 SHEET 1 B 3 ILE A 285 GLU A 286 0 SHEET 2 B 3 PRO A 548 SER A 552 -1 O ILE A 549 N ILE A 285 SHEET 3 B 3 ARG A 526 LEU A 529 -1 N GLU A 528 O VAL A 550 SHEET 1 C 2 VAL A 449 ILE A 451 0 SHEET 2 C 2 VAL A 454 ILE A 456 -1 O ILE A 456 N VAL A 449 SHEET 1 D 2 THR A 534 VAL A 535 0 SHEET 2 D 2 TYR A 544 LYS A 546 -1 O ARG A 545 N THR A 534 LINK SG CYS A 503 FE HEM A 601 1555 1555 2.38 LINK FE HEM A 601 N1 IMD A 602 1555 1555 2.20 CISPEP 1 PRO A 242 PRO A 243 0 9.21 SITE 1 AC1 19 ALA A 237 LEU A 238 HIS A 245 ARG A 249 SITE 2 AC1 19 PHE A 388 ILE A 396 PRO A 437 GLN A 438 SITE 3 AC1 19 PHE A 441 ARG A 443 SER A 495 PHE A 496 SITE 4 AC1 19 GLY A 497 HIS A 501 CYS A 503 SER A 509 SITE 5 AC1 19 IMD A 602 1PE A 603 HOH A 710 SITE 1 AC2 4 MET A 394 HEM A 601 1PE A 603 HOH A 762 SITE 1 AC3 9 GLY A 223 TRP A 224 LEU A 238 MET A 324 SITE 2 AC3 9 GLN A 325 GLN A 438 HEM A 601 IMD A 602 SITE 3 AC3 9 HOH A 719 CRYST1 136.120 136.120 75.130 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 0.007346 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007346 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013310 0.00000