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Open data
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Basic information
Entry | Database: PDB / ID: 1ocz | ||||||
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Title | BOVINE HEART CYTOCHROME C OXIDASE IN AZIDE-BOUND STATE | ||||||
![]() | (CYTOCHROME C ...) x 13 | ||||||
![]() | OXIDOREDUCTASE / OXIDOREDUCTASE (CYTOCHROME(C)-OXYGEN) / CYTOCHROME C OXIDASE / AZIDE-BOUND | ||||||
Function / homology | ![]() TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / cytochrome-c oxidase / : ...TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / cytochrome-c oxidase / : / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Mitochondrial protein degradation / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / central nervous system development / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tsukihara, T. / Yao, M. | ||||||
![]() | ![]() Title: Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase. Authors: Yoshikawa, S. / Shinzawa-Itoh, K. / Nakashima, R. / Yaono, R. / Yamashita, E. / Inoue, N. / Yao, M. / Fei, M.J. / Libeu, C.P. / Mizushima, T. / Yamaguchi, H. / Tomizaki, T. / Tsukihara, T. #1: ![]() 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. #2: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 706.6 KB | Display | ![]() |
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PDB format | ![]() | 596.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 759.2 KB | Display | ![]() |
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Full document | ![]() | 884.3 KB | Display | |
Data in XML | ![]() | 83.4 KB | Display | |
Data in CIF | ![]() | 124.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper: (Code: given Matrix: (-0.994558, -0.000845, 0.10418), Vector: Details | THIS ENZYME IS A MULTI-COMPONENT PROTEIN COMPLEX AND IS A HOMODIMER. EACH MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND TWO AZIDE MOLECULES AND SEVEN METAL CENTERS: HEME A, HEME A3, CUA, CUB, MG, NA, AND ZN. THE SIDE CHAINS OF H240 AND Y244 OF SUBUNITS A AND N ARE LINKED TOGETHER BY A COVALENT BOND. THE ELECTRON DENSITY OF REGION FROM D(Q)1 TO D(Q)3, H(U)1 TO H(U)10, J(W)57 TO J(W)59, K(X)1 TO K(X)5, K(X)55 TO K(X)56 AND M(Z)44 TO M(Z)46 IS NOISY AND VERY POOR. THOSE RESIDUES CAN NOT BE MODELLED. | |
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Components
-CYTOCHROME C ... , 13 types, 26 molecules ANBOCPDQERFSGTHUIVJWKXLYMZ
#1: Protein | Mass: 57065.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. AZIDE-BOUND STATE. Source: (natural) ![]() ![]() #2: Protein | Mass: 26040.393 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. AZIDE-BOUND STATE. Source: (natural) ![]() ![]() #3: Protein | Mass: 29943.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. AZIDE-BOUND STATE. Source: (natural) ![]() ![]() #4: Protein | Mass: 17179.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. AZIDE-BOUND STATE. Source: (natural) ![]() ![]() #5: Protein | Mass: 12453.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. AZIDE-BOUND STATE. Source: (natural) ![]() ![]() #6: Protein | Mass: 10684.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. AZIDE-BOUND STATE. Source: (natural) ![]() ![]() #7: Protein | Mass: 9452.687 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. AZIDE-BOUND STATE. Source: (natural) ![]() ![]() #8: Protein | Mass: 10039.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. AZIDE-BOUND STATE. Source: (natural) ![]() ![]() #9: Protein | Mass: 8494.982 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. AZIDE-BOUND STATE. Source: (natural) ![]() ![]() #10: Protein | Mass: 6682.726 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. AZIDE-BOUND STATE. Source: (natural) ![]() ![]() #11: Protein | Mass: 6365.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. AZIDE-BOUND STATE. Source: (natural) ![]() ![]() #12: Protein/peptide | Mass: 5449.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. AZIDE-BOUND STATE. Source: (natural) ![]() ![]() #13: Protein/peptide | Mass: 4967.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THIS ENZYME IS A HYBRID PROTEIN COMPLEX AND IS A HOMODIMER. AZIDE-BOUND STATE. Source: (natural) ![]() ![]() |
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-Non-polymers , 6 types, 20 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/ZN.gif)
#14: Chemical | ChemComp-CU / #15: Chemical | #16: Chemical | #17: Chemical | ChemComp-AZI / #18: Chemical | ChemComp-HEA / #19: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72 % / Description: OSCILLATION METHOD FOR DATA COLLECTION |
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Crystal grow | pH: 6.8 / Details: pH 6.8 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: May 19, 1996 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→100 Å / Num. obs: 270061 / % possible obs: 89.2 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 46.51 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.35→2.46 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 72 |
Reflection | *PLUS Highest resolution: 2.9 Å / Num. obs: 133932 / % possible obs: 85.7 % / Redundancy: 4.2 % / Num. measured all: 561728 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 66.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 10237 / Num. measured obs: 30449 |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 38.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→7 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS / Weight Biso : 2 / Weight position: 300 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.193 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38.292 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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