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Open data
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Basic information
Entry | Database: PDB / ID: 3e2j | ||||||
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Title | Crystal structure of bovine coupling factor B | ||||||
![]() | ATP synthase subunit s, mitochondrial | ||||||
![]() | ELECTRON TRANSPORT / leucine-rich repeat / CF0 / Hydrogen ion transport / Inner membrane / Ion transport / Membrane / Mitochondrion / Transit peptide / Transport | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Stroud, R.M. / Lee, J.K. / Belogrudov, G.I. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148.3 KB | Display | ![]() |
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PDB format | ![]() | 117.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.8 KB | Display | ![]() |
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Full document | ![]() | 486.7 KB | Display | |
Data in XML | ![]() | 29.4 KB | Display | |
Data in CIF | ![]() | 39.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dzeSC ![]() 3e3zC ![]() 3e4gC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 1 - 175 / Label seq-ID: 2 - 176
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Components
#1: Protein | Mass: 20442.676 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P22027, H+-transporting two-sector ATPase #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.4 Details: 45% PPG 400, 100 mM Bis-Tris pH 6.5, pH 7.4, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 12, 2006 / Details: KOHZU |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.111 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 16810 / % possible obs: 95.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.076 / Χ2: 1.003 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.581 / Num. unique all: 1349 / Χ2: 1.006 / % possible all: 78.3 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 36.86 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3DZE Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.854 / WRfactor Rfree: 0.314 / WRfactor Rwork: 0.223 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.724 / SU B: 24.598 / SU ML: 0.478 / SU Rfree: 0.585 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.585 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 102.76 Å2 / Biso mean: 69.806 Å2 / Biso min: 29.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 1326 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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