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- PDB-1occ: STRUCTURE OF BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDI... -

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Basic information

Entry
Database: PDB / ID: 1occ
TitleSTRUCTURE OF BOVINE HEART CYTOCHROME C OXIDASE AT THE FULLY OXIDIZED STATE
Components(CYTOCHROME C ...) x 13
KeywordsOXIDOREDUCTASE (CYTOCHROME(C)-OXYGEN) / CYTOCHROME C OXIDASE
Function / homology
Function and homology information


Complex IV assembly / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / oxidative phosphorylation ...Complex IV assembly / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Mitochondrial protein degradation / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / central nervous system development / respiratory electron transport chain / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Cytochrome C Oxidase; Chain F / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I ...Cytochrome C Oxidase; Chain F / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome C Oxidase; Chain G / Cytochrome c oxidase, subunit VIa / Cytochrome C Oxidase; Chain M / Cytochrome C Oxidase; Chain L / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit III, four-helix bundle / Cytochrome C Oxidase; Chain J / Helix Hairpins - #90 / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome C oxidase chain VIIB / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Helix Hairpins - #70 / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cupredoxins - blue copper proteins / Cupredoxin / Four Helix Bundle (Hemerythrin (Met), subunit A) / Few Secondary Structures / Irregular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Helix Hairpins / Alpha Horseshoe / Arc Repressor Mutant, subunit A / Up-down Bundle / Immunoglobulin-like
Similarity search - Domain/homology
COPPER (II) ION / HEME-A / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 6C ...COPPER (II) ION / HEME-A / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsTsukihara, T. / Aoyama, H. / Yamashita, E. / Tomizaki, T. / Yamaguchi, H. / Shinzawa-Itoh, K. / Nakashima, R. / Yaono, R. / Yoshikawa, S.
Citation
Journal: Science / Year: 1996
Title: The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A.
Authors: Tsukihara, T. / Aoyama, H. / Yamashita, E. / Tomizaki, T. / Yamaguchi, H. / Shinzawa-Itoh, K. / Nakashima, R. / Yaono, R. / Yoshikawa, S.
#1: Journal: Science / Year: 1995
Title: Structures of Metal Sites of Oxidized Bovine Heart Cytochrome C Oxidase at 2.8 A
Authors: Tsukihara, T. / Aoyama, H. / Yamashita, E. / Tomizaki, T. / Yamaguchi, H. / Shinzawa-Itoh, K. / Nakashima, R. / Yaono, R. / Yoshikawa, S.
History
DepositionApr 18, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C OXIDASE
B: CYTOCHROME C OXIDASE
C: CYTOCHROME C OXIDASE
D: CYTOCHROME C OXIDASE
E: CYTOCHROME C OXIDASE
F: CYTOCHROME C OXIDASE
G: CYTOCHROME C OXIDASE
H: CYTOCHROME C OXIDASE
I: CYTOCHROME C OXIDASE
J: CYTOCHROME C OXIDASE
K: CYTOCHROME C OXIDASE
L: CYTOCHROME C OXIDASE
M: CYTOCHROME C OXIDASE
N: CYTOCHROME C OXIDASE
O: CYTOCHROME C OXIDASE
P: CYTOCHROME C OXIDASE
Q: CYTOCHROME C OXIDASE
R: CYTOCHROME C OXIDASE
S: CYTOCHROME C OXIDASE
T: CYTOCHROME C OXIDASE
U: CYTOCHROME C OXIDASE
V: CYTOCHROME C OXIDASE
W: CYTOCHROME C OXIDASE
X: CYTOCHROME C OXIDASE
Y: CYTOCHROME C OXIDASE
Z: CYTOCHROME C OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)413,60940
Polymers409,63726
Non-polymers3,97214
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area117760 Å2
ΔGint-989 kcal/mol
Surface area121840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.100, 210.500, 178.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99386, -0.001, 0.11065), (0.00089, -1, -0.00101), (0.11065, -0.0009, 0.99386)
Vector: 170.59108, 638.15674, -9.16846)
DetailsTHIS ENZYME IS A MULTI-COMPONENT PROTEIN COMPLEX AND IS A HOMODIMER. EACH MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS: HEME A, HEME A3, CUA, CUB, MG, AND ZN. THE DEPOSITOR PROVIDED THE COORDINATES OF ONE MONOMER. THE PDB GENERATED THE OTHER MONOMER FROM THE MONOMER THAT WAS DEPOSITED USING THE TRANSFORMATION PROVIDED BY THE DEPOSITOR.

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Components

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CYTOCHROME C ... , 13 types, 26 molecules ANBOCPDQERFSGTHUIVJWKXLYMZ

#1: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 57065.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00396, cytochrome-c oxidase
#2: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 26040.393 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P68530, cytochrome-c oxidase
#3: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 29943.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00415, cytochrome-c oxidase
#4: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 17179.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00423, cytochrome-c oxidase
#5: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 12453.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00426, cytochrome-c oxidase
#6: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 10684.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00428, cytochrome-c oxidase
#7: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 9452.687 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P07471, cytochrome-c oxidase
#8: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 10039.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00429, cytochrome-c oxidase
#9: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 8494.982 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P04038, cytochrome-c oxidase
#10: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 6682.726 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P07470, cytochrome-c oxidase
#11: Protein CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 6365.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P13183, cytochrome-c oxidase
#12: Protein/peptide CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 5449.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00430, cytochrome-c oxidase
#13: Protein/peptide CYTOCHROME C OXIDASE / FERROCYTOCHROME C\:OXYGEN OXIDOREDUCTASE


Mass: 4967.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THIS ENZYME IS A MULTI COMPONENT PROTEIN COMPLEX AND IS A HOMO DIMER. ONE MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SIX METAL CENTERS, HEME A, HEME A3, CUA, CUB, MG AND ZN.
Source: (natural) Bos taurus (domestic cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P10175, cytochrome-c oxidase

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Non-polymers , 4 types, 14 molecules

#14: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#16: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#17: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 4.34 Å3/Da / Density % sol: 71.64 % / Description: OSCILLATION METHOD
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 %decyl maltoside11
240 mMsodium phosphate11
39.0 %(w/v)protein11
4PEG400011

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 155505 / % possible obs: 88.8 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.78 / Net I/σ(I): 19.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.2 / % possible all: 69.6
Reflection shell
*PLUS
% possible obs: 69.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
TSUKISCALE (LOCAL)data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
TSUKISCALE (LOCAL)data scaling
X-PLOR3.1phasing
RefinementResolution: 2.8→10 Å / σ(F): 1
Details: THE ELECTRON DENSITY OF REGION FROM G 1 TO G11 IS NOISY AND THE MODEL OF THIS REGION HAS AMBIGUITY. THE REGIONS FROM H 46 TO H 51 AND FROM H 39 TO H 42 HAVE WEAK ELECTRON DENSITIES. THE ...Details: THE ELECTRON DENSITY OF REGION FROM G 1 TO G11 IS NOISY AND THE MODEL OF THIS REGION HAS AMBIGUITY. THE REGIONS FROM H 46 TO H 51 AND FROM H 39 TO H 42 HAVE WEAK ELECTRON DENSITIES. THE ELECTRON DENSITY OF REGION FROM G 1 TO G11 IS NOISY AND THE MODEL OF THIS REGION HAS AMBIGUITY. THE REGIONS FROM H 46 TO H 51 AND FROM H 39 TO H 42 HAVE WEAK ELECTRON DENSITIES.
RfactorNum. reflection% reflection
Rfree0.252 -5 %
Rwork0.201 --
obs0.201 151622 88.7 %
Displacement parametersBiso mean: 25 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14238 0 125 0 14363
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.579
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.99
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.296
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.296

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