HEADER METAL BINDING PROTEIN 13-JAN-07 2JE3 TITLE CYTOCHROME P460 FROM NITROSOMONAS EUROPAEA - PROBABLE PHYSIOLOGICAL TITLE 2 FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P460; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 27-198; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: PROTEIN-HEME CROSS-LINK FROM NZ OF LYS 70 TO CHA OF COMPND 7 HEC 200. PROTEIN-HEME CROSSLINK FROM SG OF CYS 136 TO CAB OF HEC 200. COMPND 8 PROTEIN-HEME CROSSLINK FROM SG OF CYS 139 TO CAC OF HEC 200 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NITROSOMONAS EUROPAEA; SOURCE 3 ORGANISM_TAXID: 915; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 OTHER_DETAILS: CONTAINS ADDITIONAL N-TERMINAL METHIONINE AND AT THE SOURCE 8 TERMINUS THE ADDITIONS RESIDUES KLAAALEHHHHHH KEYWDS HEME P460, CYTOCHROME P460, CROSS-LINKED HEME, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.R.PEARSON,B.O.ELMORE,C.YANG,J.D.FERRARA,A.B.HOOPER,C.M.WILMOT REVDAT 5 16-OCT-24 2JE3 1 REMARK REVDAT 4 01-MAY-24 2JE3 1 LINK REVDAT 3 24-FEB-09 2JE3 1 VERSN REVDAT 2 17-JUL-07 2JE3 1 JRNL REVDAT 1 03-JUL-07 2JE3 0 JRNL AUTH A.R.PEARSON,B.O.ELMORE,C.YANG,J.D.FERRARA,A.B.HOOPER, JRNL AUTH 2 C.M.WILMOT JRNL TITL THE CRYSTAL STRUCTURE OF CYTOCHROME P460 OF NITROSOMONAS JRNL TITL 2 EUROPAEA REVEALS A NOVEL CYTOCHROME FOLD AND HEME-PROTEIN JRNL TITL 3 CROSS-LINK. JRNL REF BIOCHEMISTRY V. 46 8340 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17583915 JRNL DOI 10.1021/BI700086R REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 17341 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 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 : 921 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 775 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1223 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 138 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.01000 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): 0.130 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.126 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1336 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1837 ; 1.653 ; 2.057 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 162 ; 7.688 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 57 ;38.380 ;24.211 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 201 ;13.866 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;19.111 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 191 ; 0.141 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1024 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 646 ; 0.260 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 901 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 104 ; 0.151 ; 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): 54 ; 0.170 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 25 ; 0.169 ; 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): 807 ; 1.006 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1277 ; 1.729 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 622 ; 2.206 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 554 ; 3.367 ; 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. RESIDUES 31-40 AND 82-85 ARE NOT VISIBLE IN THE REMARK 3 ELECTRON DENSITY REMARK 4 REMARK 4 2JE3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1290031092. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.20 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : VARIMAX CONFOCAL MAXFLUX REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17344 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 43.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.1 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 15.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.10 REMARK 200 R MERGE FOR SHELL (I) : 0.10000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 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: INITIAL MODEL FROM SULPHUR SAD STRUCTURE REMARK 200 REMARK 200 REMARK: THE STRUCTURE WAS SOLVED BY SAD USING A DATASET COLLECTED REMARK 200 AT CR K-ALPHA. PHASED USING SHELX AND SHARP. THE INITIAL MODEL REMARK 200 WAS THEN USED TO PHASE THE HIGHER RESOLUTION CU K-ALPHA DATASET REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.20 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 42.34433 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 84.68867 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 84.68867 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 42.34433 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 0 REMARK 465 ASN A 31 REMARK 465 GLU A 32 REMARK 465 LEU A 33 REMARK 465 ASN A 34 REMARK 465 ASP A 35 REMARK 465 GLY A 36 REMARK 465 LYS A 37 REMARK 465 ALA A 38 REMARK 465 PRO A 39 REMARK 465 PHE A 40 REMARK 465 GLY A 82 REMARK 465 SER A 83 REMARK 465 GLY A 84 REMARK 465 PRO A 171 REMARK 465 LYS A 172 REMARK 465 LYS A 173 REMARK 465 LEU A 174 REMARK 465 ALA A 175 REMARK 465 ALA A 176 REMARK 465 ALA A 177 REMARK 465 LEU A 178 REMARK 465 GLU A 179 REMARK 465 HIS A 180 REMARK 465 HIS A 181 REMARK 465 HIS A 182 REMARK 465 HIS A 183 REMARK 465 HIS A 184 REMARK 465 HIS A 185 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 2044 O HOH A 2048 2.04 REMARK 500 SG CYS A 139 CAC HEC A 1171 2.18 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 ASP A 121 N - CA - C ANGL. DEV. = 18.1 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 ASP A 121 77.96 -23.66 REMARK 500 CYS A 136 -64.84 -134.79 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 PRO A 120 ASP A 121 -137.29 REMARK 500 ASP A 121 THR A 122 133.75 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 HEC A1171 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 140 NE2 REMARK 620 2 HEC A1171 NA 99.8 REMARK 620 3 HEC A1171 NB 91.7 86.7 REMARK 620 4 HEC A1171 NC 94.0 165.4 88.3 REMARK 620 5 HEC A1171 ND 100.1 93.6 167.9 88.5 REMARK 620 6 PO4 A1172 O2 174.5 74.7 87.2 91.3 81.3 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 PO4 A1172 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A1173 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A1174 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A1171 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JE2 RELATED DB: PDB REMARK 900 CYTOCHROME P460 FROM NITROSOMONAS EUROPAEA - PROBABLE REMARK 900 NONPHYSIOLOGICAL OXIDIZED FORM REMARK 999 REMARK 999 SEQUENCE REMARK 999 RECOMBINANT PROTEIN CONTAINS ADDITIONAL N-TERMINAL REMARK 999 METHIONINE AND C-TERMINAL TAG KLAAALEHHHHHH DBREF 2JE3 A 0 0 PDB 2JE3 2JE3 0 0 DBREF 2JE3 A 1 172 UNP Q50927 Q50927_NITEU 27 198 DBREF 2JE3 A 173 185 PDB 2JE3 2JE3 173 185 SEQRES 1 A 186 MET ALA GLY VAL ALA GLU PHE ASN ASP LYS GLY GLU LEU SEQRES 2 A 186 LEU LEU PRO LYS ASN TYR ARG GLU TRP VAL MET VAL GLY SEQRES 3 A 186 THR GLN VAL THR PRO ASN GLU LEU ASN ASP GLY LYS ALA SEQRES 4 A 186 PRO PHE THR GLU ILE ARG THR VAL TYR VAL ASP PRO GLU SEQRES 5 A 186 SER TYR ALA HIS TRP LYS LYS THR GLY GLU PHE ARG ASP SEQRES 6 A 186 GLY THR VAL THR VAL LYS GLU LEU VAL SER VAL GLY ASP SEQRES 7 A 186 ARG LYS GLY PRO GLY SER GLY ASN GLY TYR PHE MET GLY SEQRES 8 A 186 ASP TYR ILE GLY LEU GLU ALA SER VAL LYS ASP SER GLN SEQRES 9 A 186 ARG PHE ALA ASN GLU PRO GLY ASN TRP ALA PHE TYR ILE SEQRES 10 A 186 PHE TYR VAL PRO ASP THR PRO LEU VAL ALA ALA ALA LYS SEQRES 11 A 186 ASN LEU PRO THR ALA GLU CYS ALA ALA CYS HIS LYS GLU SEQRES 12 A 186 ASN ALA LYS THR ASP MET VAL PHE THR GLN PHE TYR PRO SEQRES 13 A 186 VAL LEU ARG ALA ALA LYS ALA THR GLY GLU SER GLY VAL SEQRES 14 A 186 VAL ALA PRO LYS LYS LEU ALA ALA ALA LEU GLU HIS HIS SEQRES 15 A 186 HIS HIS HIS HIS HET HEC A1171 43 HET PO4 A1172 5 HET PO4 A1173 5 HET PO4 A1174 5 HETNAM HEC HEME C HETNAM PO4 PHOSPHATE ION FORMUL 2 HEC C34 H34 FE N4 O4 FORMUL 3 PO4 3(O4 P 3-) FORMUL 6 HOH *138(H2 O) HELIX 1 1 ASN A 17 TRP A 21 5 5 HELIX 2 2 ASP A 49 GLY A 60 1 12 HELIX 3 3 GLU A 108 GLY A 110 5 3 HELIX 4 4 CYS A 136 ALA A 144 1 9 HELIX 5 5 PHE A 150 PHE A 153 5 4 HELIX 6 6 TYR A 154 GLY A 164 1 11 SHEET 1 AA 2 LEU A 12 LEU A 13 0 SHEET 2 AA 2 ALA A 127 ALA A 128 -1 O ALA A 128 N LEU A 12 SHEET 1 AB 5 VAL A 22 THR A 29 0 SHEET 2 AB 5 GLU A 42 VAL A 48 -1 O GLU A 42 N THR A 29 SHEET 3 AB 5 VAL A 67 ARG A 78 -1 O VAL A 69 N TYR A 47 SHEET 4 AB 5 GLY A 86 LYS A 100 -1 O GLY A 86 N ARG A 78 SHEET 5 AB 5 TRP A 112 TYR A 118 -1 O ALA A 113 N VAL A 99 LINK NZ LYS A 70 CHA HEC A1171 1555 1555 1.63 LINK SG CYS A 136 CAB HEC A1171 1555 1555 1.96 LINK NE2 HIS A 140 FE HEC A1171 1555 1555 2.16 LINK FE HEC A1171 O2 PO4 A1172 1555 1555 2.62 CISPEP 1 GLY A 80 PRO A 81 0 -6.18 SITE 1 AC1 3 GLU A 96 HEC A1171 HOH A2132 SITE 1 AC2 10 TRP A 56 ASN A 107 LYS A 145 THR A 146 SITE 2 AC2 10 THR A 151 ARG A 158 LYS A 161 HOH A2134 SITE 3 AC2 10 HOH A2135 HOH A2136 SITE 1 AC3 5 ASP A 8 PRO A 109 LYS A 141 HOH A2137 SITE 2 AC3 5 HOH A2138 SITE 1 AC4 21 GLN A 27 ARG A 44 THR A 68 LYS A 70 SITE 2 AC4 21 ARG A 78 PRO A 81 GLU A 96 SER A 98 SITE 3 AC4 21 TYR A 115 ILE A 116 GLU A 135 CYS A 136 SITE 4 AC4 21 CYS A 139 HIS A 140 MET A 148 VAL A 149 SITE 5 AC4 21 PHE A 150 TYR A 154 PO4 A1172 HOH A2067 SITE 6 AC4 21 HOH A2131 CRYST1 53.256 53.256 127.033 90.00 90.00 120.00 P 31 2 1 6 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 0.018777 0.010841 0.000000 0.00000 SCALE2 0.000000 0.021682 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007872 0.00000