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Yorodumi- PDB-3e3z: Crystal structure of bovine coupling Factor B bound with phenylar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e3z | ||||||
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Title | Crystal structure of bovine coupling Factor B bound with phenylarsine oxide | ||||||
Components | ATP synthase subunit s, mitochondrial | ||||||
Keywords | ELECTRON TRANSPORT / leucine-rich repeat / CF0 / Hydrogen ion transport / Inner membrane / Ion transport / Membrane / Mitochondrion / Transit peptide / Transport | ||||||
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: 1.7 Å | ||||||
Authors | Stroud, R.M. / Lee, J.K. / 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 | 3e3z.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e3z.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 3e3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e3z_validation.pdf.gz | 432.2 KB | Display | wwPDB validaton report |
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Full document | 3e3z_full_validation.pdf.gz | 433.7 KB | Display | |
Data in XML | 3e3z_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 3e3z_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/3e3z ftp://data.pdbj.org/pub/pdb/validation_reports/e3/3e3z | HTTPS FTP |
-Related structure data
Related structure data | 3dzeSC 3e2jC 3e4gC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20514.738 Da / Num. of mol.: 1 / Mutation: G28E 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-MG / |
#3: Chemical | ChemComp-TRS / |
#4: Chemical | ChemComp-PA0 / |
#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: 2.25 Å3/Da / Density % sol: 45.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 8 Details: 50% PPG 400, 100 mM Tris-HCl pH 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: 0.97946 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 12, 2007 / Details: KOHZU | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→40 Å / Num. obs: 19212 / % possible obs: 95.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.039 / Χ2: 1.004 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DZE Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.16 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.894 / SU B: 1.758 / SU ML: 0.06 / SU R Cruickshank DPI: 0.101 / SU Rfree: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.101 / 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 max: 57.46 Å2 / Biso mean: 8.605 Å2 / Biso min: 4.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.745 Å / Total num. of bins used: 20
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