[English] 日本語
Yorodumi- PDB-4cbk: The c-ring ion binding site of the ATP synthase from Bacillus pse... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cbk | ||||||
---|---|---|---|---|---|---|---|
Title | The c-ring ion binding site of the ATP synthase from Bacillus pseudofirmus OF4 is adapted to alkaliphilic cell physiology | ||||||
Components | ATP SYNTHASE SUBUNIT C | ||||||
Keywords | TRANSFERASE / F1FO-ATP SYNTHASE / C-RING ROTOR / ION BINDING POCKET | ||||||
Function / homology | Function and homology information proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / plasma membrane Similarity search - Function | ||||||
Biological species | BACILLUS PSEUDOFIRMUS OF4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | ||||||
Authors | Preiss, L. / Yildiz, O. / Meier, T. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2014 Title: The C-Ring Ion-Binding Site of the ATP Synthase from Bacillus Pseudofirmus of4 is Adapted to Alkaliphilic Lifestyle. Authors: Preiss, L. / Langer, J.D. / Hicks, D.B. / Liu, J. / Yildiz, O. / Krulwich, T.A. / Meier, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4cbk.cif.gz | 174.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4cbk.ent.gz | 143.7 KB | Display | PDB format |
PDBx/mmJSON format | 4cbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/4cbk ftp://data.pdbj.org/pub/pdb/validation_reports/cb/4cbk | HTTPS FTP |
---|
-Related structure data
Related structure data | 4cbjC 2x2vS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 6987.461 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) BACILLUS PSEUDOFIRMUS OF4 (bacteria) / References: UniProt: P22483 #2: Chemical | ChemComp-DPV / #3: Chemical | ChemComp-NA / #4: Sugar | ChemComp-LMT / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.48 Å3/Da / Density % sol: 72.57 % / Description: NONE |
---|---|
Crystal grow | pH: 9 / Details: pH 9 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8551 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 3, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8551 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→40 Å / Num. obs: 60954 / % possible obs: 99.3 % / Observed criterion σ(I): 1.84 / Redundancy: 4.53 % / Biso Wilson estimate: 42.68 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 12.33 |
Reflection shell | Resolution: 2.42→2.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.84 / % possible all: 99 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X2V Resolution: 2.42→40.004 Å / SU ML: 0.22 / σ(F): 1.99 / Phase error: 22.5 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.42→40.004 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|