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Yorodumi- PDB-3s39: Structure of Thermus thermophilus cytochrome ba3 oxidase 60s afte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s39 | ||||||
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Title | Structure of Thermus thermophilus cytochrome ba3 oxidase 60s after Xe depressurization | ||||||
Components |
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Keywords | OXIDOREDUCTASE / xenon | ||||||
Function / homology | Function and homology information cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / : / copper ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.8 Å | ||||||
Authors | Luna, V.M. / Fee, J.A. / Deniz, A.A. / Stout, C.D. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Mobility of Xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase. Authors: Luna, V.M. / Fee, J.A. / Deniz, A.A. / Stout, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s39.cif.gz | 149.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s39.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 3s39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/3s39 ftp://data.pdbj.org/pub/pdb/validation_reports/s3/3s39 | HTTPS FTP |
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-Related structure data
Related structure data | 3s33C 3s38C 3s3aC 3s3bC 3s3cC 3s3dC 1xmeS C: citing same article (ref.) 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: 63401.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: cbaa / Plasmid: PMK18 / Production host: Thermus thermophilus (bacteria) / Strain (production host): HB8 / References: UniProt: Q5SJ79, cytochrome-c oxidase |
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#2: Protein | Mass: 18350.975 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: cbab, cbac / Plasmid: PMK18 / Production host: Thermus thermophilus (bacteria) / Strain (production host): HB8 / References: UniProt: Q5SJ80, cytochrome-c oxidase |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 3638.407 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: cbad / Plasmid: PMK18 / Production host: Thermus thermophilus (bacteria) / Strain (production host): HB8 / References: UniProt: P82543, cytochrome-c oxidase |
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-Non-polymers , 5 types, 8 molecules
#4: Chemical | ChemComp-CU / | ||
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#5: Chemical | ChemComp-HEM / | ||
#6: Chemical | ChemComp-HAS / | ||
#7: Chemical | ChemComp-XE / #8: Chemical | ChemComp-CUA / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.59 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12-17% PEG 2000, 0-200mM KCl, 15-60mM bis-Tris pH 7.0, 6.5mM nonyl-B-D-glucopyranoside, vapor diffusion, hanging drop, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4.8→56.8 Å / Num. all: 6087 / Num. obs: 6087 / % possible obs: 99.7 % / Redundancy: 20.4 % / Rsym value: 0.124 / Net I/σ(I): 13.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XME Resolution: 4.8→56.8 Å / Cor.coef. Fo:Fc: 0.852 / Cor.coef. Fo:Fc free: 0.864 / WRfactor Rfree: 0.3338 / WRfactor Rwork: 0.2778 / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.7249 / SU B: 135.068 / SU ML: 1.48 / SU Rfree: 1.6992 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.709 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 200.17 Å2 / Biso mean: 200.17 Å2 / Biso min: 200.17 Å2
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Refinement step | Cycle: LAST / Resolution: 4.8→56.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.801→4.925 Å / Total num. of bins used: 20
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