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Yorodumi- PDB-5ndc: Structure of ba3-type cytochrome c oxidase from Thermus thermophi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ndc | ||||||||||||
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Title | Structure of ba3-type cytochrome c oxidase from Thermus thermophilus by serial femtosecond crystallography | ||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / Cytochrome c oxidase / SFX / Respiratory chain enzyme | ||||||||||||
Function / homology | Function and homology information cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / respirasome / membrane => GO:0016020 / copper ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Thermus thermophilus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||||||||
Authors | Andersson, R. / Safari, C. / Dods, R. / Nango, E. / Tanaka, R. / Nakane, T. / Tono, K. / Joti, Y. / Bath, P. / Dunevall, E. ...Andersson, R. / Safari, C. / Dods, R. / Nango, E. / Tanaka, R. / Nakane, T. / Tono, K. / Joti, Y. / Bath, P. / Dunevall, E. / Bosman, E. / Nureki, O. / Iwata, S. / Neutze, R. / Branden, G. | ||||||||||||
Funding support | Sweden, 3items
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Citation | Journal: Sci Rep / Year: 2017 Title: Serial femtosecond crystallography structure of cytochrome c oxidase at room temperature. Authors: Andersson, R. / Safari, C. / Dods, R. / Nango, E. / Tanaka, R. / Yamashita, A. / Nakane, T. / Tono, K. / Joti, Y. / Bath, P. / Dunevall, E. / Bosman, R. / Nureki, O. / Iwata, S. / Neutze, R. / Branden, G. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ndc.cif.gz | 317.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ndc.ent.gz | 253.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ndc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/5ndc ftp://data.pdbj.org/pub/pdb/validation_reports/nd/5ndc | HTTPS FTP |
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-Related structure data
Related structure data | 3s8fS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Cytochrome c oxidase subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 63540.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: cbaA, TTHA1135 / Production host: Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJ79, cytochrome-c oxidase |
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#2: Protein | Mass: 18581.299 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: cbaB, ctaC, TTHA1134 / Production host: Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJ80, cytochrome-c oxidase |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 3769.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: HGMM_F04D06C07, TTMY_0198 / Production host: Thermus thermophilus HB8 (bacteria) / References: UniProt: A0A1J1EEV7, UniProt: P82543*PLUS |
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-Non-polymers , 6 types, 111 molecules
#4: Chemical | ChemComp-CU / | ||||
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#5: Chemical | ChemComp-HEM / | ||||
#6: Chemical | ChemComp-HAS / | ||||
#7: Chemical | ChemComp-OLC / ( #8: Chemical | ChemComp-CUA / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.69 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5.3 Details: 100mM sodium cacodylate trihydrate pH 5.3, 37% PEG400, 1.4M NaCl Room temperature for 2-3 days |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.6314 Å |
Detector | Type: MPCCD / Detector: CCD / Date: Feb 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.6314 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→36.4 Å / Num. all: 1864107 / Num. obs: 50602 / % possible obs: 100 % / Redundancy: 14.7 % / CC1/2: 0.956 / R split: 0.1937 / Net I/σ(I): 3.74 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 14.7 % / CC1/2: 0.366 / R split: 1.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3S8F Resolution: 2.3→36.4 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 14.121 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.446 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→36.4 Å
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Refine LS restraints |
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