+Open data
-Basic information
Entry | Database: PDB / ID: 3dze | ||||||
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Title | Crystal structure of bovine coupling Factor B bound with cadmium | ||||||
Components | ATP synthase subunit s, mitochondrial | ||||||
Keywords | ELECTRON TRANSPORT / leucine-rich repeat / CF(0) / Hydrogen ion transport / Ion transport / Membrane / Mitochondrion / Mitochondrion inner membrane / Transit peptide / Transport / TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information ATP biosynthetic process / Formation of ATP by chemiosmotic coupling / Cristae formation / proton-transporting ATP synthase complex, coupling factor F(o) / proton transmembrane transport / mitochondrial inner membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å | ||||||
Authors | Lee, J.K. / Stroud, R.M. / Belogrudov, G.I. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Crystal structure of bovine mitochondrial factor B at 0.96-A resolution. Authors: Lee, J.K. / Belogrudov, G.I. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dze.cif.gz | 100.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dze.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 3dze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/3dze ftp://data.pdbj.org/pub/pdb/validation_reports/dz/3dze | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20514.738 Da / Num. of mol.: 1 / Mutation: G3E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: ATP5S, ATPW / Plasmid: pET43 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P22027, H+-transporting two-sector ATPase |
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#2: Chemical | ChemComp-TRS / |
#3: Chemical | ChemComp-CD / |
#4: Chemical | ChemComp-MG / |
#5: 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: 2.29 Å3/Da / Density % sol: 46.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: 50% PPG 400, 100 mM Tris, pH 7.4-8.0, vapor diffusion, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.0332 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 12, 2007 / Details: KOHZU: Double Crystal Si(111) |
Radiation | Monochromator: KOHZU: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→40 Å / Num. obs: 62817 / % possible obs: 83.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.036 / Rsym value: 0.027 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 1.84 / Rsym value: 0.279 / % possible all: 11.3 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→30 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 0.853 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.965 Å2
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Refinement step | Cycle: LAST / Resolution: 1.15→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.18 Å / Total num. of bins used: 20
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