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- PDB-2zvy: Structure of the periplasmic domain of MotB from Salmonella (crys... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zvy | ||||||
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Title | Structure of the periplasmic domain of MotB from Salmonella (crystal form II) | ||||||
![]() | Chemotaxis protein motB | ||||||
![]() | MEMBRANE PROTEIN / 2-layer sandwich / Bacterial flagellum / Cell inner membrane / Cell membrane / Chemotaxis / Flagellar rotation / Membrane / Transmembrane | ||||||
Function / homology | ![]() archaeal or bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kojima, S. / Homma, M. / Namba, K. / Imada, K. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.2 KB | Display | ![]() |
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PDB format | ![]() | 71.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.6 KB | Display | ![]() |
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Full document | ![]() | 446.6 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 31.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zovSC ![]() 2zvzC 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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Unit cell |
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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.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.42 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.0914 Å2 / ksol: 0.314714 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→35.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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