HEADER METAL BINDING PROTEIN 08-JUN-08 3DE9 TITLE CRYSTAL STRUCTURE OF A TRIMERIC CYTOCHROME CB562 ASSEMBLY INDUCED BY TITLE 2 NICKEL COORDINATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUBLE CYTOCHROME B562; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOCHROME B-562; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: CYBC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NI-STABILIZED TRIMERIC SUPERSTRUCTURE, ELECTRON TRANSPORT, HEME, KEYWDS 2 IRON, METAL-BINDING, PERIPLASM, TRANSPORT, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.N.SALGADO,R.A.LEWIS,A.L.RHEINGOLD,F.A.TEZCAN REVDAT 4 21-FEB-24 3DE9 1 REMARK REVDAT 3 20-OCT-21 3DE9 1 REMARK SEQADV REVDAT 2 07-MAR-18 3DE9 1 REMARK REVDAT 1 21-APR-09 3DE9 0 JRNL AUTH E.N.SALGADO,R.A.LEWIS,S.MOSSIN,A.L.RHEINGOLD,F.A.TEZCAN JRNL TITL CONTROL OF PROTEIN OLIGOMERIZATION SYMMETRY BY METAL JRNL TITL 2 COORDINATION: C2 AND C3 SYMMETRICAL ASSEMBLIES THROUGH JRNL TITL 3 CU(II) AND NI(II) COORDINATION. JRNL REF INORG.CHEM. V. 48 2726 2009 JRNL REFN ISSN 0020-1669 JRNL PMID 19267481 JRNL DOI 10.1021/IC9001237 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 6918 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) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 519 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) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 513 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE SET COUNT : 38 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 819 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 55 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.09000 REMARK 3 B22 (A**2) : 0.09000 REMARK 3 B33 (A**2) : -0.14000 REMARK 3 B12 (A**2) : 0.05000 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): 0.243 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.213 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.177 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.385 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 884 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 763 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1201 ; 1.918 ; 2.114 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1791 ; 1.002 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 105 ; 5.848 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 42 ;43.565 ;26.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 154 ;18.885 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;12.339 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 125 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 978 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 137 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 248 ; 0.239 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 790 ; 0.176 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 417 ; 0.171 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 479 ; 0.096 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 35 ; 0.193 ; 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): 29 ; 0.214 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 17 ; 0.312 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.224 ; 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): 681 ; 1.311 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 213 ; 0.265 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 845 ; 1.547 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 404 ; 2.829 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 354 ; 3.898 ; 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 : BABINET MODEL WITH 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 3DE9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000047929. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER APEX II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7513 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.49200 REMARK 200 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS, 23% PEG 4000, 4.16 MM REMARK 280 NISO4, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.52100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.73456 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.65700 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 25.52100 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 14.73456 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 40.65700 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 25.52100 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 14.73456 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.65700 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 29.46911 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 81.31400 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 29.46911 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 81.31400 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 29.46911 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 81.31400 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -140.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 -25.52100 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -44.20367 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 25.52100 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 -44.20367 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NI NI A 107 LIES ON A SPECIAL POSITION. REMARK 375 NI NI A 108 LIES ON A SPECIAL POSITION. 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 SG CYS A 101 CAC HEM A 150 1.67 REMARK 500 SG CYS A 98 CAB HEM A 150 1.77 REMARK 500 OD1 ASP A 2 N GLU A 4 2.14 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 LYS A 83 79.12 -100.85 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 NI A 109 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 1 N REMARK 620 2 ALA A 1 O 78.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 150 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 7 SD REMARK 620 2 HEM A 150 NA 93.0 REMARK 620 3 HEM A 150 NB 85.6 89.9 REMARK 620 4 HEM A 150 NC 91.3 175.5 91.3 REMARK 620 5 HEM A 150 ND 98.2 95.1 173.5 83.3 REMARK 620 6 HIS A 102 NE2 176.4 90.5 94.5 85.1 81.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 107 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 59 NE2 REMARK 620 2 HIS A 63 NE2 81.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 108 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 73 NE2 REMARK 620 2 HIS A 77 NE2 91.1 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 108 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 109 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 150 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QLA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A 16-HELIX BUNDLE ARCHITECTURE PRODUCED BY THE REMARK 900 ZINC-MEDIATED SELF ASSEMBLY OF FOUR CYTOCHROME CB562 MOLECULES REMARK 900 RELATED ID: 2BC5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI CYTOCHROME B562 WITH ENGINEERED C-TYPE REMARK 900 HEME LINKAGES REMARK 900 RELATED ID: 3DE8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A DIMERIC CYTOCHROME CB562 ASSEMBLY INDUCED BY REMARK 900 COPPER COORDINATION DBREF 3DE9 A 1 106 UNP P0ABE7 C562_ECOLX 23 128 SEQADV 3DE9 HIS A 59 UNP P0ABE7 LYS 81 ENGINEERED MUTATION SEQADV 3DE9 HIS A 73 UNP P0ABE7 ASP 95 ENGINEERED MUTATION SEQADV 3DE9 HIS A 77 UNP P0ABE7 LYS 99 ENGINEERED MUTATION SEQADV 3DE9 CYS A 98 UNP P0ABE7 ARG 120 ENGINEERED MUTATION SEQADV 3DE9 CYS A 101 UNP P0ABE7 TYR 123 ENGINEERED MUTATION SEQRES 1 A 106 ALA ASP LEU GLU ASP ASN MET GLU THR LEU ASN ASP ASN SEQRES 2 A 106 LEU LYS VAL ILE GLU LYS ALA ASP ASN ALA ALA GLN VAL SEQRES 3 A 106 LYS ASP ALA LEU THR LYS MET ARG ALA ALA ALA LEU ASP SEQRES 4 A 106 ALA GLN LYS ALA THR PRO PRO LYS LEU GLU ASP LYS SER SEQRES 5 A 106 PRO ASP SER PRO GLU MET HIS ASP PHE ARG HIS GLY PHE SEQRES 6 A 106 ASP ILE LEU VAL GLY GLN ILE HIS ASP ALA LEU HIS LEU SEQRES 7 A 106 ALA ASN GLU GLY LYS VAL LYS GLU ALA GLN ALA ALA ALA SEQRES 8 A 106 GLU GLN LEU LYS THR THR CYS ASN ALA CYS HIS GLN LYS SEQRES 9 A 106 TYR ARG HET NI A 107 1 HET NI A 108 1 HET NI A 109 1 HET HEM A 150 43 HETNAM NI NICKEL (II) ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 NI 3(NI 2+) FORMUL 5 HEM C34 H32 FE N4 O4 FORMUL 6 HOH *55(H2 O) HELIX 1 1 ASP A 2 LYS A 19 1 18 HELIX 2 2 ASN A 22 GLN A 41 1 20 HELIX 3 3 PRO A 45 GLU A 49 5 5 HELIX 4 4 SER A 55 GLU A 81 1 27 HELIX 5 5 LYS A 83 LEU A 94 1 12 HELIX 6 6 LEU A 94 ARG A 106 1 13 LINK N ALA A 1 NI NI A 109 1555 1555 2.03 LINK O ALA A 1 NI NI A 109 1555 1555 2.03 LINK SD MET A 7 FE HEM A 150 1555 1555 2.31 LINK NE2 HIS A 59 NI NI A 107 1555 1555 2.24 LINK NE2 HIS A 63 NI NI A 107 1555 1555 2.09 LINK NE2 HIS A 73 NI NI A 108 1555 1555 2.21 LINK NE2 HIS A 77 NI NI A 108 1555 1555 2.19 LINK NE2 HIS A 102 FE HEM A 150 1555 1555 2.01 SITE 1 AC1 2 HIS A 59 HIS A 63 SITE 1 AC2 2 HIS A 73 HIS A 77 SITE 1 AC3 3 ALA A 1 ASP A 39 LYS A 42 SITE 1 AC4 15 LEU A 3 GLU A 4 MET A 7 LEU A 14 SITE 2 AC4 15 PRO A 45 PRO A 46 PHE A 61 GLY A 64 SITE 3 AC4 15 PHE A 65 CYS A 98 CYS A 101 HIS A 102 SITE 4 AC4 15 TYR A 105 ARG A 106 HOH A 154 CRYST1 51.042 51.042 121.971 90.00 90.00 120.00 H 3 9 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 0.019592 0.011311 0.000000 0.00000 SCALE2 0.000000 0.022623 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008199 0.00000