[English] 日本語
Yorodumi- PDB-2zvy: Structure of the periplasmic domain of MotB from Salmonella (crys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zvy | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the periplasmic domain of MotB from Salmonella (crystal form II) | ||||||
Components | Chemotaxis protein motB | ||||||
Keywords | MEMBRANE PROTEIN / 2-layer sandwich / Bacterial flagellum / Cell inner membrane / Cell membrane / Chemotaxis / Flagellar rotation / Membrane / Transmembrane | ||||||
Function / homology | Function and homology information archaeal or bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Kojima, S. / Homma, M. / Namba, K. / Imada, K. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2009 Title: Stator assembly and activation mechanism of the flagellar motor by the periplasmic region of MotB Authors: Kojima, S. / Imada, K. / Sakuma, M. / Sudo, Y. / Kojima, C. / Minamino, T. / Homma, M. / Namba, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2zvy.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2zvy.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 2zvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zvy_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2zvy_full_validation.pdf.gz | 446.6 KB | Display | |
Data in XML | 2zvy_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 2zvy_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/2zvy ftp://data.pdbj.org/pub/pdb/validation_reports/zv/2zvy | HTTPS FTP |
-Related structure data
Related structure data | 2zovSC 2zvzC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20734.672 Da / Num. of mol.: 2 / Fragment: C-terminal fragment 2 (UNP residues 99 -276 ) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: SJW1103 / Gene: motB / Plasmid: PET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55892 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.42 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% PEG 4000, 0.1M Tris-HCl, 0.2M Sodium Acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 35 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2008 |
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→35.97 Å / Num. all: 36833 / Num. obs: 36833 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.01 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 5341 / Rsym value: 0.314 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZOV Resolution: 1.75→35.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1558926.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.0914 Å2 / ksol: 0.314714 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→35.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|