+Open data
-Basic information
Entry | Database: PDB / ID: 1ocr | ||||||
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Title | BOVINE HEART CYTOCHROME C OXIDASE IN THE FULLY REDUCED STATE | ||||||
Components | (CYTOCHROME C ...) x 13 | ||||||
Keywords | OXIDOREDUCTASE / OXIDOREDUCTASE (CYTOCHROME(C)-OXYGEN) / CYTOCHROME C OXIDASE / REDUCED | ||||||
Function / homology | Function and homology information TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly / Cytoprotection by HMOX1 / respiratory chain complex IV / regulation of oxidative phosphorylation / Respiratory electron transport / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase ...TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly / Cytoprotection by HMOX1 / respiratory chain complex IV / regulation of oxidative phosphorylation / Respiratory electron transport / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / electron transport coupled proton transport / cytochrome-c oxidase activity / ATP synthesis coupled electron transport / enzyme regulator activity / central nervous system development / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / nucleoplasm / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.35 Å | ||||||
Authors | Tsukihara, T. / Yao, M. | ||||||
Citation | Journal: Science / Year: 1998 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: 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. #2: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ocr.cif.gz | 704.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ocr.ent.gz | 594.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ocr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/1ocr ftp://data.pdbj.org/pub/pdb/validation_reports/oc/1ocr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.993679, -0.001063, 0.112252), Vector: Details | THIS ENZYME IS A MULTI-COMPONENT PROTEIN COMPLEX AND IS A HOMODIMER. EACH MONOMER IS COMPOSED OF 13 DIFFERENT SUBUNITS AND SEVEN METAL CENTERS: HEME A, HEME A3, CUA, CUB, MG, NA, AND ZN. THE SIDE CHAINS OF H 240 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)6, 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 CANNOT BE MODELLED. | |
-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. FULLY REDUCED STATE. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00396, cytochrome-c oxidase #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. FULLY REDUCED STATE. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P68530, cytochrome-c oxidase #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. FULLY REDUCED STATE. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00415, cytochrome-c oxidase #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. FULLY REDUCED STATE. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00423, cytochrome-c oxidase #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. FULLY REDUCED STATE. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00426, cytochrome-c oxidase #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. FULLY REDUCED STATE. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00428, cytochrome-c oxidase #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. FULLY REDUCED STATE. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P07471, cytochrome-c oxidase #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. FULLY REDUCED STATE. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00429, cytochrome-c oxidase #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. FULLY REDUCED STATE. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P04038, cytochrome-c oxidase #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. FULLY REDUCED STATE. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P07470, cytochrome-c oxidase #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. FULLY REDUCED STATE. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P13183, cytochrome-c oxidase #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. FULLY REDUCED STATE. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00430, cytochrome-c oxidase #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. FULLY REDUCED STATE. Source: (natural) Bos taurus (cattle) / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P10175, cytochrome-c oxidase |
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-Non-polymers , 5 types, 16 molecules
#14: Chemical | ChemComp-CU / #15: Chemical | #16: Chemical | #17: Chemical | ChemComp-HEA / #18: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
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: 36.56 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 Num. measured all: 1184694 |
Reflection shell | *PLUS % possible obs: 72 % / Num. unique obs: 28814 / Num. measured obs: 55541 / Rmerge(I) obs: 0.32 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.35→15 Å / Rfactor Rfree error: 0.0021 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: GAUSS / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 40.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS / Rms dev Biso : 2 Å2 / Rms dev position: 300 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.35→2.46 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.84 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.211 / Rfactor Rfree: 0.251 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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