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PDBsum entry 3bvd

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Top Page protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
3bvd
Jmol
Contents
Protein chains
550 a.a.
166 a.a.
33 a.a.
Ligands
HEM
HAS
CUA
Metals
_XE ×7
_CU
HEADER    OXIDOREDUCTASE                          07-JAN-08   3BVD
TITLE     STRUCTURE OF SURFACE-ENGINEERED CYTOCHROME BA3 OXIDASE FROM
TITLE    2 THERMUS THERMOPHILUS UNDER XENON PRESSURE, 100PSI 5MIN
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: CYTOCHROME C OXIDASE SUBUNIT 1;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE I, CYTOCHROME C
COMPND   5 BA3, SUBUNIT I, CYTOCHROME CBA3 SUBUNIT 1;
COMPND   6 EC: 1.9.3.1;
COMPND   7 ENGINEERED: YES;
COMPND   8 MUTATION: YES;
COMPND   9 MOL_ID: 2;
COMPND  10 MOLECULE: CYTOCHROME C OXIDASE SUBUNIT 2;
COMPND  11 CHAIN: B;
COMPND  12 SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE II, CYTOCHROME C
COMPND  13 BA3, SUBUNIT II, CYTOCHROME CBA3 SUBUNIT 2;
COMPND  14 EC: 1.9.3.1;
COMPND  15 ENGINEERED: YES;
COMPND  16 MUTATION: YES;
COMPND  17 MOL_ID: 3;
COMPND  18 MOLECULE: CYTOCHROME C OXIDASE POLYPEPTIDE 2A;
COMPND  19 CHAIN: C;
COMPND  20 SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE IIA, CYTOCHROME
COMPND  21 C BA3, SUBUNIT IIA, CYTOCHROME CBA3 SUBUNIT 2A;
COMPND  22 EC: 1.9.3.1;
COMPND  23 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS;
SOURCE   3 STRAIN: HB8;
SOURCE   4 ATCC: 27634;
SOURCE   5 GENE: CBAA;
SOURCE   6 EXPRESSION_SYSTEM: THERMUS THERMOPHILUS;
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: HB8;
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE   9 EXPRESSION_SYSTEM_PLASMID: PMK18;
SOURCE  10 MOL_ID: 2;
SOURCE  11 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS;
SOURCE  12 STRAIN: HB8;
SOURCE  13 ATCC: 27634;
SOURCE  14 GENE: CBAB, CTAC;
SOURCE  15 EXPRESSION_SYSTEM: THERMUS THERMOPHILUS;
SOURCE  16 EXPRESSION_SYSTEM_STRAIN: HB8;
SOURCE  17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  18 EXPRESSION_SYSTEM_PLASMID: PMK18;
SOURCE  19 MOL_ID: 3;
SOURCE  20 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS;
SOURCE  21 STRAIN: HB8;
SOURCE  22 ATCC: 27634;
SOURCE  23 GENE: CBAD;
SOURCE  24 EXPRESSION_SYSTEM: THERMUS THERMOPHILUS;
SOURCE  25 EXPRESSION_SYSTEM_STRAIN: HB8;
SOURCE  26 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  27 EXPRESSION_SYSTEM_PLASMID: PMK18
KEYWDS    CYTOCHROME BA3 OXIDASE, HEME, INTEGRAL MEMBRANE PROTEIN,
KEYWDS   2 COPPER, ELECTRON TRANSPORT, HYDROGEN ION TRANSPORT, ION
KEYWDS   3 TRANSPORT, IRON, METAL-BINDING, OXIDOREDUCTASE, RESPIRATORY
KEYWDS   4 CHAIN, TRANSMEMBRANE, TRANSPORT, FORMYLATION, XENON
EXPDTA    X-RAY DIFFRACTION
AUTHOR    V.M.LUNA,Y.CHEN,J.A.FEE,C.D.STOUT
REVDAT   2   24-FEB-09 3BVD    1       VERSN
REVDAT   1   20-MAY-08 3BVD    0
JRNL        AUTH   V.M.LUNA,Y.CHEN,J.A.FEE,C.D.STOUT
JRNL        TITL   CRYSTALLOGRAPHIC STUDIES OF XE AND KR BINDING
JRNL        TITL 2 WITHIN THE LARGE INTERNAL CAVITY OF CYTOCHROME BA3
JRNL        TITL 3 FROM THERMUS THERMOPHILUS: STRUCTURAL ANALYSIS AND
JRNL        TITL 4 ROLE OF OXYGEN TRANSPORT CHANNELS IN THE HEME-CU
JRNL        TITL 5 OXIDASES.
JRNL        REF    BIOCHEMISTRY                  V.  47  4657 2008
JRNL        REFN                   ISSN 0006-2960
JRNL        PMID   18376849
JRNL        DOI    10.1021/BI800045Y
REMARK   1
REMARK   1 REFERENCE 1
REMARK   1  AUTH   B.LIU,V.M.LUNA,Y.CHEN,C.D.STOUT,J.A.FEE
REMARK   1  TITL   AN UNEXPECTED OUTCOME OF SURFACE ENGINEERING AN
REMARK   1  TITL 2 INTEGRAL MEMBRANE PROTEIN: IMPROVED
REMARK   1  TITL 3 CRYSTALLIZATION OF CYTOCHROME BA3 FROM THERMUS
REMARK   1  TITL 4 THERMOPHILUS
REMARK   1  REF    ACTA CRYSTALLOGR.,SECT.F      V.  63  1029 2007
REMARK   1  REFN                   ESSN 1744-3091
REMARK   1  PMID   18084085
REMARK   1  DOI    10.1107/S1744309107054176
REMARK   1 REFERENCE 2
REMARK   1  AUTH   L.M.HUNSICKER-WANG,R.L.PACOMA,Y.CHEN,J.A.FEE,
REMARK   1  AUTH 2 C.D.STOUT
REMARK   1  TITL   A NOVEL CRYOPROTECTION SCHEME FOR ENCHANCING THE
REMARK   1  TITL 2 DIFFRACTION OF CRYSTALS OF RECOMBINANT CYTOCHROME
REMARK   1  TITL 3 BA3 OXIDASE FROM THERMUS THERMOPHILUS
REMARK   1  REF    ACTA CRYSTALLOGR.,SECT.D      V.  61   340 2005
REMARK   1  REFN                   ISSN 0907-4449
REMARK   1  PMID   15735345
REMARK   1  DOI    10.1107/S0907444904033906
REMARK   2
REMARK   2 RESOLUTION.    3.37 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.2.0019, CNS
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,
REMARK   3               : READ,RICE,SIMONSON,WARREN
REMARK   3
REMARK   3  REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 3.37
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 26.96
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 99.8
REMARK   3   NUMBER OF REFLECTIONS             : 16329
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 SET) : 0.292
REMARK   3   FREE R VALUE                     : 0.336
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.100
REMARK   3   FREE R VALUE TEST SET COUNT      : 823
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL
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) : 3.37
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 3.58
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 100.00
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 2513
REMARK   3   BIN R VALUE           (WORKING SET) : 0.3490
REMARK   3   BIN FREE R VALUE                    : 0.4420
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 147
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 5907
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 118
REMARK   3   SOLVENT ATOMS            : 0
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 108.22
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 85.48
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -0.04000
REMARK   3    B22 (A**2) : -0.04000
REMARK   3    B33 (A**2) : 0.07000
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 COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL
REMARK   3   ESD FROM SIGMAA              (A) : NULL
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : NULL
REMARK   3   BOND ANGLES            (DEGREES) : NULL
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : OVERALL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED : MASK
REMARK   3   KSOL        : NULL
REMARK   3   BSOL        : NULL
REMARK   3
REMARK   3  NCS MODEL : NULL
REMARK   3
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  PARAMETER FILE  1  : NULL
REMARK   3  TOPOLOGY FILE  1   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE
REMARK   3  RIDING POSITIONS
REMARK   4
REMARK   4 3BVD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-08.
REMARK 100 THE RCSB ID CODE IS RCSB046002.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 02-FEB-07
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 7.0
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : SSRL
REMARK 200  BEAMLINE                       : BL9-1
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.979
REMARK 200  MONOCHROMATOR                  : SIDE-SCATTERING CUBEROOT I-
REMARK 200                                   BEAM BENT SINGLE CRYSTAL;
REMARK 200                                   ASYMMETRIC CUT 12.2 DEGS.
REMARK 200  OPTICS                         : VERTICAL FOCUSING MIRROR;
REMARK 200                                   SINGLE CRYSTAL SI(311) BENT
REMARK 200                                   MONOCHROMATOR (HORIZONTAL
REMARK 200                                   FOCUSING)
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 315
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200  DATA SCALING SOFTWARE          : SCALA
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 16341
REMARK 200  RESOLUTION RANGE HIGH      (A) : 3.370
REMARK 200  RESOLUTION RANGE LOW       (A) : 27.160
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.7
REMARK 200  DATA REDUNDANCY                : 4.500
REMARK 200  R MERGE                    (I) : 0.06800
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 8.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.37
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 3.55
REMARK 200  COMPLETENESS FOR SHELL     (%) : 100.0
REMARK 200  DATA REDUNDANCY IN SHELL       : 4.80
REMARK 200  R MERGE FOR SHELL          (I) : 0.46300
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : 1.800
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP, REFMAC 5.2.0019, CNS, COOT
REMARK 200 STARTING MODEL: PDB ENTRY 1XME
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 61.65
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 6-9% PEG 2000, 50MM KCL, 7.5-30MM
REMARK 280  BIS-TRIS PH 7.0, 6.5MM NONYL-B-D-GLUCOPYRANOSIDE , VAPOR
REMARK 280  DIFFUSION, TEMPERATURE 297K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,-Y,Z+1/2
REMARK 290       3555   -Y+1/2,X+1/2,Z+1/4
REMARK 290       4555   Y+1/2,-X+1/2,Z+3/4
REMARK 290       5555   -X+1/2,Y+1/2,-Z+1/4
REMARK 290       6555   X+1/2,-Y+1/2,-Z+3/4
REMARK 290       7555   Y,X,-Z
REMARK 290       8555   -Y,-X,-Z+1/2
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        0.00000
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       76.76750
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       59.86300
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       59.86300
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       38.38375
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       59.86300
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       59.86300
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000      115.15125
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       59.86300
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       59.86300
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       38.38375
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       59.86300
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       59.86300
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000      115.15125
REMARK 290   SMTRY1   7  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   8  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000       76.76750
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: 14360 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 25190 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -149.8 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
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    -5
REMARK 465     HIS A    -4
REMARK 465     HIS A    -3
REMARK 465     HIS A    -2
REMARK 465     HIS A    -1
REMARK 465     HIS A     0
REMARK 465     HIS A     1
REMARK 465     ALA A     2
REMARK 465     VAL A     3
REMARK 465     ARG A     4
REMARK 465     ALA A     5
REMARK 465     SER A     6
REMARK 465     GLU A     7
REMARK 465     ILE A     8
REMARK 465     SER A     9
REMARK 465     ARG A    10
REMARK 465     VAL A    11
REMARK 465     TYR A    12
REMARK 465     MET B     1
REMARK 465     VAL B     2
REMARK 465     MET C     1
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    ASN A  98      -21.01     75.77
REMARK 500    ASN A 102       95.43    -56.57
REMARK 500    THR A 130       74.64    -63.12
REMARK 500    LEU A 132      160.57     70.38
REMARK 500    PHE A 135       59.19     37.36
REMARK 500    PRO A 278       47.14    -83.09
REMARK 500    PRO A 292      -37.15    -39.12
REMARK 500    ARG A 330      -89.47   -105.36
REMARK 500    TRP A 341        3.83    -68.43
REMARK 500    SER A 368       42.23    -87.15
REMARK 500    PHE A 369      -94.41     48.38
REMARK 500    GLN A 388      -64.79   -105.30
REMARK 500    SER A 391      -73.81   -103.45
REMARK 500    SER A 400       23.99    -71.46
REMARK 500    SER A 414     -150.76    -80.64
REMARK 500    ASN A 446       13.79     81.54
REMARK 500    VAL A 456       78.36   -118.92
REMARK 500    LEU A 483      -35.94    -35.77
REMARK 500    PHE A 489       38.22    -78.40
REMARK 500    GLU A 496       47.26    -77.78
REMARK 500    PRO A 499       24.36    -68.24
REMARK 500    PRO A 505      156.08    -49.98
REMARK 500    HIS A 552       21.64   -143.25
REMARK 500    GLN B   4      -89.67     58.20
REMARK 500    HIS B   8      -29.00   -147.67
REMARK 500    THR B  41       -8.88    -57.52
REMARK 500    THR B  57       46.66   -108.66
REMARK 500    PRO B  63       -9.53    -58.09
REMARK 500    ALA B  65      -60.82    -90.36
REMARK 500    THR B  74       32.53   -141.52
REMARK 500    PHE B  86     -167.35   -120.97
REMARK 500    ALA B  87       83.60    -58.61
REMARK 500    PHE B  88       41.40     70.13
REMARK 500    ASP B 111      -82.06   -149.42
REMARK 500    LYS B 167      179.21    -57.82
REMARK 500    LYS C   4      103.68     68.10
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 800  FE
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A  72   NE2
REMARK 620 2 HIS A 386   NE2 178.3
REMARK 620 N                    1
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              CU A 803  CU
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 282   NE2
REMARK 620 2 HIS A 283   NE2  94.9
REMARK 620 N                    1
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                             CUA B 802  CU1
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLN B 151   O
REMARK 620 2 HIS B 157   ND1  84.6
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 CU A 803
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HAS A 801
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CUA B 802
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 805
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 807
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 808
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 809
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 810
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2QPD   RELATED DB: PDB
REMARK 900 SURFACE-ENGINEERED CYTOCHROME BA3 OXIDASE
DBREF  3BVD A    2   562  UNP    Q5SJ79   COX1_THET8       2    562
DBREF  3BVD B    1   168  UNP    Q5SJ80   COX2_THET8       1    168
DBREF  3BVD C    1    34  UNP    P82543   COXA_THET8       1     34
SEQADV 3BVD MET A   -5  UNP  Q5SJ79              EXPRESSION TAG
SEQADV 3BVD HIS A   -4  UNP  Q5SJ79              EXPRESSION TAG
SEQADV 3BVD HIS A   -3  UNP  Q5SJ79              EXPRESSION TAG
SEQADV 3BVD HIS A   -2  UNP  Q5SJ79              EXPRESSION TAG
SEQADV 3BVD HIS A   -1  UNP  Q5SJ79              EXPRESSION TAG
SEQADV 3BVD HIS A    0  UNP  Q5SJ79              EXPRESSION TAG
SEQADV 3BVD HIS A    1  UNP  Q5SJ79              EXPRESSION TAG
SEQADV 3BVD ARG A  258  UNP  Q5SJ79    LYS   258 ENGINEERED
SEQADV 3BVD GLN B    4  UNP  Q5SJ80    GLU     4 ENGINEERED
SEQRES   1 A  568  MET HIS HIS HIS HIS HIS HIS ALA VAL ARG ALA SER GLU
SEQRES   2 A  568  ILE SER ARG VAL TYR GLU ALA TYR PRO GLU LYS LYS ALA
SEQRES   3 A  568  THR LEU TYR PHE LEU VAL LEU GLY PHE LEU ALA LEU ILE
SEQRES   4 A  568  VAL GLY SER LEU PHE GLY PRO PHE GLN ALA LEU ASN TYR
SEQRES   5 A  568  GLY ASN VAL ASP ALA TYR PRO LEU LEU LYS ARG LEU LEU
SEQRES   6 A  568  PRO PHE VAL GLN SER TYR TYR GLN GLY LEU THR LEU HIS
SEQRES   7 A  568  GLY VAL LEU ASN ALA ILE VAL PHE THR GLN LEU PHE ALA
SEQRES   8 A  568  GLN ALA ILE MET VAL TYR LEU PRO ALA ARG GLU LEU ASN
SEQRES   9 A  568  MET ARG PRO ASN MET GLY LEU MET TRP LEU SER TRP TRP
SEQRES  10 A  568  MET ALA PHE ILE GLY LEU VAL VAL ALA ALA LEU PRO LEU
SEQRES  11 A  568  LEU ALA ASN GLU ALA THR VAL LEU TYR THR PHE TYR PRO
SEQRES  12 A  568  PRO LEU LYS GLY HIS TRP ALA PHE TYR LEU GLY ALA SER
SEQRES  13 A  568  VAL PHE VAL LEU SER THR TRP VAL SER ILE TYR ILE VAL
SEQRES  14 A  568  LEU ASP LEU TRP ARG ARG TRP LYS ALA ALA ASN PRO GLY
SEQRES  15 A  568  LYS VAL THR PRO LEU VAL THR TYR MET ALA VAL VAL PHE
SEQRES  16 A  568  TRP LEU MET TRP PHE LEU ALA SER LEU GLY LEU VAL LEU
SEQRES  17 A  568  GLU ALA VAL LEU PHE LEU LEU PRO TRP SER PHE GLY LEU
SEQRES  18 A  568  VAL GLU GLY VAL ASP PRO LEU VAL ALA ARG THR LEU PHE
SEQRES  19 A  568  TRP TRP THR GLY HIS PRO ILE VAL TYR PHE TRP LEU LEU
SEQRES  20 A  568  PRO ALA TYR ALA ILE ILE TYR THR ILE LEU PRO LYS GLN
SEQRES  21 A  568  ALA GLY GLY ARG LEU VAL SER ASP PRO MET ALA ARG LEU
SEQRES  22 A  568  ALA PHE LEU LEU PHE LEU LEU LEU SER THR PRO VAL GLY
SEQRES  23 A  568  PHE HIS HIS GLN PHE ALA ASP PRO GLY ILE ASP PRO THR
SEQRES  24 A  568  TRP LYS MET ILE HIS SER VAL LEU THR LEU PHE VAL ALA
SEQRES  25 A  568  VAL PRO SER LEU MET THR ALA PHE THR VAL ALA ALA SER
SEQRES  26 A  568  LEU GLU PHE ALA GLY ARG LEU ARG GLY GLY ARG GLY LEU
SEQRES  27 A  568  PHE GLY TRP ILE ARG ALA LEU PRO TRP ASP ASN PRO ALA
SEQRES  28 A  568  PHE VAL ALA PRO VAL LEU GLY LEU LEU GLY PHE ILE PRO
SEQRES  29 A  568  GLY GLY ALA GLY GLY ILE VAL ASN ALA SER PHE THR LEU
SEQRES  30 A  568  ASP TYR VAL VAL HIS ASN THR ALA TRP VAL PRO GLY HIS
SEQRES  31 A  568  PHE HIS LEU GLN VAL ALA SER LEU VAL THR LEU THR ALA
SEQRES  32 A  568  MET GLY SER LEU TYR TRP LEU LEU PRO ASN LEU THR GLY
SEQRES  33 A  568  LYS PRO ILE SER ASP ALA GLN ARG ARG LEU GLY LEU ALA
SEQRES  34 A  568  VAL VAL TRP LEU TRP PHE LEU GLY MET MET ILE MET ALA
SEQRES  35 A  568  VAL GLY LEU HIS TRP ALA GLY LEU LEU ASN VAL PRO ARG
SEQRES  36 A  568  ARG ALA TYR ILE ALA GLN VAL PRO ASP ALA TYR PRO HIS
SEQRES  37 A  568  ALA ALA VAL PRO MET VAL PHE ASN VAL LEU ALA GLY ILE
SEQRES  38 A  568  VAL LEU LEU VAL ALA LEU LEU LEU PHE ILE TYR GLY LEU
SEQRES  39 A  568  PHE SER VAL LEU LEU SER ARG GLU ARG LYS PRO GLU LEU
SEQRES  40 A  568  ALA GLU ALA PRO LEU PRO PHE ALA GLU VAL ILE SER GLY
SEQRES  41 A  568  PRO GLU ASP ARG ARG LEU VAL LEU ALA MET ASP ARG ILE
SEQRES  42 A  568  GLY PHE TRP PHE ALA VAL ALA ALA ILE LEU VAL VAL LEU
SEQRES  43 A  568  ALA TYR GLY PRO THR LEU VAL GLN LEU PHE GLY HIS LEU
SEQRES  44 A  568  ASN PRO VAL PRO GLY TRP ARG LEU TRP
SEQRES   1 B  168  MET VAL ASP GLN HIS LYS ALA HIS LYS ALA ILE LEU ALA
SEQRES   2 B  168  TYR GLU LYS GLY TRP LEU ALA PHE SER LEU ALA MET LEU
SEQRES   3 B  168  PHE VAL PHE ILE ALA LEU ILE ALA TYR THR LEU ALA THR
SEQRES   4 B  168  HIS THR ALA GLY VAL ILE PRO ALA GLY LYS LEU GLU ARG
SEQRES   5 B  168  VAL ASP PRO THR THR VAL ARG GLN GLU GLY PRO TRP ALA
SEQRES   6 B  168  ASP PRO ALA GLN ALA VAL VAL GLN THR GLY PRO ASN GLN
SEQRES   7 B  168  TYR THR VAL TYR VAL LEU ALA PHE ALA PHE GLY TYR GLN
SEQRES   8 B  168  PRO ASN PRO ILE GLU VAL PRO GLN GLY ALA GLU ILE VAL
SEQRES   9 B  168  PHE LYS ILE THR SER PRO ASP VAL ILE HIS GLY PHE HIS
SEQRES  10 B  168  VAL GLU GLY THR ASN ILE ASN VAL GLU VAL LEU PRO GLY
SEQRES  11 B  168  GLU VAL SER THR VAL ARG TYR THR PHE LYS ARG PRO GLY
SEQRES  12 B  168  GLU TYR ARG ILE ILE CYS ASN GLN TYR CYS GLY LEU GLY
SEQRES  13 B  168  HIS GLN ASN MET PHE GLY THR ILE VAL VAL LYS GLU
SEQRES   1 C   34  MET GLU GLU LYS PRO LYS GLY ALA LEU ALA VAL ILE LEU
SEQRES   2 C   34  VAL LEU THR LEU THR ILE LEU VAL PHE TRP LEU GLY VAL
SEQRES   3 C   34  TYR ALA VAL PHE PHE ALA ARG GLY
HET     CU  A 803       1
HET    HEM  A 800      43
HET    HAS  A 801      65
HET    CUA  B 802       2
HET     XE  A 805       1
HET     XE  A 806       1
HET     XE  A 807       1
HET     XE  A 808       1
HET     XE  A 809       1
HET     XE  A 810       1
HET     XE  A 811       1
HETNAM      CU COPPER (II) ION
HETNAM     HEM PROTOPORPHYRIN IX CONTAINING FE
HETNAM     HAS HEME-AS
HETNAM     CUA DINUCLEAR COPPER ION
HETNAM      XE XENON
HETSYN     HEM HEME
FORMUL   4   CU    CU 2+
FORMUL   5  HEM    C34 H32 FE N4 O4
FORMUL   6  HAS    C54 H64 FE N4 O6
FORMUL   7  CUA    CU2
FORMUL   8   XE    7(XE)
HELIX    1   1 PRO A   16  LEU A   37  1                                  22
HELIX    2   2 PHE A   38  TYR A   46  1                                   9
HELIX    3   3 ALA A   51  LEU A   59  1                                   9
HELIX    4   4 SER A   64  ILE A   78  1                                  15
HELIX    5   5 ILE A   78  ASN A   98  1                                  21
HELIX    6   6 ASN A  102  ALA A  126  1                                  25
HELIX    7   7 HIS A  142  ASN A  174  1                                  33
HELIX    8   8 PRO A  180  PHE A  207  1                                  28
HELIX    9   9 PHE A  207  GLY A  214  1                                   8
HELIX   10  10 ASP A  220  HIS A  233  1                                  14
HELIX   11  11 HIS A  233  ILE A  250  1                                  18
HELIX   12  12 ILE A  250  ALA A  255  1                                   6
HELIX   13  13 ASP A  262  SER A  276  1                                  15
HELIX   14  14 VAL A  279  GLN A  284  5                                   6
HELIX   15  15 ASP A  291  VAL A  305  1                                  15
HELIX   16  16 ALA A  306  ARG A  327  1                                  22
HELIX   17  17 ASN A  343  ALA A  367  1                                  25
HELIX   18  18 SER A  368  VAL A  375  5                                   8
HELIX   19  19 ALA A  379  HIS A  386  1                                   8
HELIX   20  20 SER A  391  SER A  400  1                                  10
HELIX   21  21 LEU A  404  GLY A  410  1                                   7
HELIX   22  22 ASP A  415  LEU A  445  1                                  31
HELIX   23  23 TYR A  452  HIS A  462  5                                  11
HELIX   24  24 ALA A  463  LEU A  492  1                                  30
HELIX   25  25 PRO A  499  ALA A  504  1                                   6
HELIX   26  26 ARG A  518  ASP A  525  1                                   8
HELIX   27  27 ARG A  526  GLY A  551  1                                  26
HELIX   28  28 ASP B    3  ALA B    7  5                                   5
HELIX   29  29 HIS B    8  THR B   39  1                                  32
HELIX   30  30 HIS B   40  ILE B   45  5                                   6
HELIX   31  31 ASP B   66  GLN B   69  5                                   4
HELIX   32  32 GLY B  156  ASN B  159  5                                   4
HELIX   33  33 PRO C    5  GLY C   34  1                                  30
SHEET    1   A 2 GLY A 218  VAL A 219  0
SHEET    2   A 2 VAL A 556  PRO A 557 -1  O  VAL A 556   N  VAL A 219
SHEET    1   B 3 VAL B  71  GLN B  73  0
SHEET    2   B 3 GLN B  78  PHE B  86 -1  O  THR B  80   N  VAL B  72
SHEET    3   B 3 GLY B  89  GLN B  91 -1  O  GLN B  91   N  LEU B  84
SHEET    1   C 4 VAL B  71  GLN B  73  0
SHEET    2   C 4 GLN B  78  PHE B  86 -1  O  THR B  80   N  VAL B  72
SHEET    3   C 4 GLU B 102  THR B 108  1  O  THR B 108   N  ALA B  85
SHEET    4   C 4 SER B 133  THR B 138 -1  O  VAL B 135   N  PHE B 105
SHEET    1   D 5 ILE B  95  VAL B  97  0
SHEET    2   D 5 PHE B 161  VAL B 166  1  O  VAL B 165   N  ILE B  95
SHEET    3   D 5 GLY B 143  ILE B 148 -1  N  ILE B 147   O  GLY B 162
SHEET    4   D 5 HIS B 114  VAL B 118 -1  N  HIS B 117   O  ILE B 148
SHEET    5   D 5 ASN B 124  VAL B 127 -1  O  VAL B 127   N  HIS B 114
LINK         NE2 HIS A  72                FE   HEM A 800     1555   1555  2.20
LINK         NE2 HIS A 282                CU    CU A 803     1555   1555  2.03
LINK         NE2 HIS A 283                CU    CU A 803     1555   1555  2.19
LINK         NE2 HIS A 386                FE   HEM A 800     1555   1555  2.11
LINK         ND1 HIS B 114                CU2  CUA B 802     1555   1555  2.29
LINK         O   GLN B 151                CU1  CUA B 802     1555   1555  2.17
LINK         ND1 HIS B 157                CU1  CUA B 802     1555   1555  2.04
CISPEP   1 PRO A  137    PRO A  138          0         9.29
CISPEP   2 GLN B   91    PRO B   92          0        -3.38
CISPEP   3 ASN B   93    PRO B   94          0         9.40
SITE     1 AC1  3 HIS A 233  HIS A 282  HIS A 283
SITE     1 AC2 20 GLY A  39  PRO A  40  GLN A  42  ALA A  43
SITE     2 AC2 20 TYR A  46  TYR A  65  LEU A  69  HIS A  72
SITE     3 AC2 20 ASN A  76  ALA A  77  TYR A 133  PHE A 385
SITE     4 AC2 20 HIS A 386  VAL A 389  ALA A 390  THR A 394
SITE     5 AC2 20 MET A 432  ARG A 449  ARG A 450  ALA A 451
SITE     1 AC3 24 TYR A 133  TRP A 229  VAL A 236  TYR A 237
SITE     2 AC3 24 TRP A 239  HIS A 282  THR A 302  SER A 309
SITE     3 AC3 24 ALA A 313  ALA A 317  LEU A 353  LEU A 354
SITE     4 AC3 24 PHE A 356  GLY A 360  GLY A 363  ASN A 366
SITE     5 AC3 24 ALA A 367  ASP A 372  HIS A 376  VAL A 381
SITE     6 AC3 24 HIS A 384  PHE A 385  GLN A 388  ARG A 449
SITE     1 AC4  6 HIS B 114  CYS B 149  GLN B 151  CYS B 153
SITE     2 AC4  6 HIS B 157  MET B 160
SITE     1 AC5  2 TYR A 133  GLY A 232
SITE     1 AC6  1 LEU A 208
SITE     1 AC7  1 VAL A 201
SITE     1 AC8  2 PHE A 228   XE A 810
SITE     1 AC9  3 PHE A 228  GLY A 232   XE A 809
CRYST1  119.726  119.726  153.535  90.00  90.00  90.00 P 41 21 2     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      0.008352  0.000000  0.000000        0.00000
SCALE2      0.000000  0.008352  0.000000        0.00000
SCALE3      0.000000  0.000000  0.006513        0.00000
      
PROCHECK
Go to PROCHECK summary
 References