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Yorodumi- PDB-8gbt: Time-resolve SFX structure of a photoproduct of carbon monoxide c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gbt | ||||||||||||
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Title | Time-resolve SFX structure of a photoproduct of carbon monoxide complex of bovine cytochrome c oxidase | ||||||||||||
Components | (Cytochrome c oxidase subunit ...) x 13 | ||||||||||||
Keywords | MEMBRANE PROTEIN / Oxidative phosphorylation / Electron transfer chain / Bioenergetics / Cytochrome c oxidase / Serial femtosecond X-ray crystallography | ||||||||||||
Function / homology | Function and homology information TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / respiratory chain complex IV / Respiratory electron transport / regulation of oxidative phosphorylation / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase ...TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / respiratory chain complex IV / Respiratory electron transport / regulation of oxidative phosphorylation / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / 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 / nucleoplasm / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) | ||||||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||||||||
Authors | Ishigami, I. / Yeh, S.-R. / Rousseau, D.L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: Detection of a Geminate Photoproduct of Bovine Cytochrome c Oxidase by Time-Resolved Serial Femtosecond Crystallography. Authors: Ishigami, I. / Carbajo, S. / Zatsepin, N. / Hikita, M. / Conrad, C.E. / Nelson, G. / Coe, J. / Basu, S. / Grant, T. / Seaberg, M.H. / Sierra, R.G. / Hunter, M.S. / Fromme, P. / Fromme, R. / ...Authors: Ishigami, I. / Carbajo, S. / Zatsepin, N. / Hikita, M. / Conrad, C.E. / Nelson, G. / Coe, J. / Basu, S. / Grant, T. / Seaberg, M.H. / Sierra, R.G. / Hunter, M.S. / Fromme, P. / Fromme, R. / Rousseau, D.L. / Yeh, S.R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gbt.cif.gz | 801.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gbt.ent.gz | 638.9 KB | Display | PDB format |
PDBx/mmJSON format | 8gbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/8gbt ftp://data.pdbj.org/pub/pdb/validation_reports/gb/8gbt | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Cytochrome c oxidase subunit ... , 13 types, 26 molecules ANBOCPDQERFSGTHUIVJWKXLYMZ
#1: Protein | Mass: 57093.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00396, cytochrome-c oxidase #2: Protein | Mass: 26068.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P68530 #3: Protein | Mass: 29957.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00415 #4: Protein | Mass: 17179.646 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00423 #5: Protein | Mass: 12453.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00426 #6: Protein | Mass: 10684.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00428 #7: Protein | Mass: 9629.782 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07471 #8: Protein | Mass: 10039.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00429 #9: Protein | Mass: 8537.019 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P04038 #10: Protein | Mass: 6682.726 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07470 #11: Protein | Mass: 6365.217 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13183 #12: Protein/peptide | Mass: 5449.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00430 #13: Protein/peptide | Mass: 4967.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P10175 |
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-Sugars , 1 types, 4 molecules
#28: Sugar | ChemComp-DMU / |
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-Non-polymers , 16 types, 299 molecules
#14: Chemical | ChemComp-HEA / #15: Chemical | #16: Chemical | #17: Chemical | #18: Chemical | ChemComp-TGL / #19: Chemical | ChemComp-PGV / ( #20: Chemical | #21: Chemical | #22: Chemical | ChemComp-CHD / #23: Chemical | #24: Chemical | ChemComp-CDL / #25: Chemical | #26: Chemical | #27: Chemical | ChemComp-PEK / ( #29: Chemical | #30: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 277 K / Method: batch mode / pH: 6.8 / Details: PEG4000, Sodium Phosphate, decylmaltoside |
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-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.321 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Jun 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.321 Å / Relative weight: 1 |
Reflection | Resolution: 1.759→32.45 Å / Num. obs: 172414 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.859 / Net I/σ(I): 6.92 |
Reflection shell | Resolution: 2.87→2.99 Å / Num. unique obs: 17697 / CC1/2: 0.226 / % possible all: 100 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→32.002 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.882 / SU B: 26.062 / SU ML: 0.458 / Cross valid method: THROUGHOUT / ESU R: 0.562 / ESU R Free: 0.334 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.179 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→32.002 Å
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Refine LS restraints |
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LS refinement shell |
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