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- PDB-3s33: Structure of Thermus thermophilus cytochrome ba3 oxidase 10s afte... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3s33 | ||||||
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Title | Structure of Thermus thermophilus cytochrome ba3 oxidase 10s after Xe depressurization | ||||||
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![]() | OXIDOREDUCTASE / xenon | ||||||
Function / homology | ![]() cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / : / copper ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Luna, V.M. / Fee, J.A. / Deniz, A.A. / Stout, C.D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.5 KB | Display | ![]() |
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PDB format | ![]() | 110.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3s38C ![]() 3s39C ![]() 3s3aC ![]() 3s3bC ![]() 3s3cC ![]() 3s3dC ![]() 1xmeS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | biological unit is the same as asym. |
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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.) ![]() ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() |
-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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 9 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HAS.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HAS.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/CUA.gif)
#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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.08 % |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 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: 4.45→90.115 Å / Num. all: 6368 / Num. obs: 6368 / % possible obs: 99.7 % / Redundancy: 23.7 % / Rsym value: 0.193 / Net I/σ(I): 11.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1XME Resolution: 4.45→45.06 Å / Cor.coef. Fo:Fc: 0.826 / Cor.coef. Fo:Fc free: 0.791 / WRfactor Rfree: 0.3428 / WRfactor Rwork: 0.2928 / Occupancy max: 1 / Occupancy min: 0.09 / FOM work R set: 0.7522 / SU B: 110.263 / SU ML: 1.412 / SU Rfree: 1.5926 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.593 / 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: 130.5 Å2 / Biso mean: 130.5 Å2 / Biso min: 130.5 Å2
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Refinement step | Cycle: LAST / Resolution: 4.45→45.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.45→4.565 Å / Total num. of bins used: 20
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