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Yorodumi- PDB-3wg7: A 1.9 angstrom radiation damage free X-ray structure of large (42... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wg7 | ||||||
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Title | A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography | ||||||
Components | (Cytochrome c oxidase subunit ...) x 13 | ||||||
Keywords | OXIDOREDUCTASE / Electron Transport Complex IV / Iron / Oxidation-Reduction / Protein Interaction Domains / Motifs / Membrane | ||||||
Function / homology | Function and homology information 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 / enzyme regulator activity / ATP synthesis coupled electron transport / central nervous system development / oxidoreductase activity / mitochondrial inner membrane / copper ion binding / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hirata, K. / Shinzawa-Itoh, K. / Yano, N. / Takemura, S. / Kato, K. / Hatanaka, M. / Muramoto, K. / Kawahara, T. / Tsukihara, T. / Yamashita, E. ...Hirata, K. / Shinzawa-Itoh, K. / Yano, N. / Takemura, S. / Kato, K. / Hatanaka, M. / Muramoto, K. / Kawahara, T. / Tsukihara, T. / Yamashita, E. / Tono, K. / Ueno, G. / Hikima, T. / Murakami, H. / Inubushi, Y. / Yabashi, M. / Ishikawa, T. / Yamamoto, M. / Ogura, T. / Sugimoto, H. / Shen, J.R. / Yoshikawa, S. / Ago, H. | ||||||
Citation | Journal: Nat.Methods / Year: 2014 Title: Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL. Authors: Hirata, K. / Shinzawa-Itoh, K. / Yano, N. / Takemura, S. / Kato, K. / Hatanaka, M. / Muramoto, K. / Kawahara, T. / Tsukihara, T. / Yamashita, E. / Tono, K. / Ueno, G. / Hikima, T. / ...Authors: Hirata, K. / Shinzawa-Itoh, K. / Yano, N. / Takemura, S. / Kato, K. / Hatanaka, M. / Muramoto, K. / Kawahara, T. / Tsukihara, T. / Yamashita, E. / Tono, K. / Ueno, G. / Hikima, T. / Murakami, H. / Inubushi, Y. / Yabashi, M. / Ishikawa, T. / Yamamoto, M. / Ogura, T. / Sugimoto, H. / Shen, J.R. / Yoshikawa, S. / Ago, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wg7.cif.gz | 845.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wg7.ent.gz | 686.9 KB | Display | PDB format |
PDBx/mmJSON format | 3wg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wg7_validation.pdf.gz | 8.4 MB | Display | wwPDB validaton report |
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Full document | 3wg7_full_validation.pdf.gz | 8.8 MB | Display | |
Data in XML | 3wg7_validation.xml.gz | 205.7 KB | Display | |
Data in CIF | 3wg7_validation.cif.gz | 266.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/3wg7 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/3wg7 | HTTPS FTP |
-Related structure data
Related structure data | 7y44C 2dyrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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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, 2 molecules
#27: Sugar |
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-Non-polymers , 14 types, 2530 molecules
#14: Chemical | ChemComp-HEA / #15: Chemical | #16: Chemical | #17: Chemical | ChemComp-NA / #18: Chemical | #19: Chemical | ChemComp-PGV / ( #20: Chemical | ChemComp-TGL / #21: Chemical | #22: Chemical | ChemComp-CHD / #23: Chemical | #24: Chemical | ChemComp-PEK / ( #25: Chemical | ChemComp-CDL / #26: Chemical | #28: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 69 |
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-Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.69 % |
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Crystal grow | Temperature: 277 K / Method: batch / pH: 5.7 Details: 40mM sodium phosphate, 0.2% decylmaltoside, pH 5.7, BATCH, temperature 277K, Batch |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.241 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.241 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 500699 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.243 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.1 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DYR Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.407 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.471 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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