+Open data
-Basic information
Entry | Database: PDB / ID: 2zf8 | ||||||
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Title | Crystal structure of MotY | ||||||
Components | Component of sodium-driven polar flagellar motor | ||||||
Keywords | STRUCTURAL PROTEIN / BETA BARREL / 2-Layer Sandwich / Flagellum | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio alginolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å | ||||||
Authors | Imada, K. / Kojima, S. / Namba, K. / Homma, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Insights into the stator assembly of the Vibrio flagellar motor from the crystal structure of MotY Authors: Kojima, S. / Shinohara, A. / Terashima, H. / Yakushi, T. / Sakuma, M. / Homma, M. / Namba, K. / Imada, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zf8.cif.gz | 58.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zf8.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 2zf8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zf8_validation.pdf.gz | 426.6 KB | Display | wwPDB validaton report |
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Full document | 2zf8_full_validation.pdf.gz | 459.6 KB | Display | |
Data in XML | 2zf8_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 2zf8_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/2zf8 ftp://data.pdbj.org/pub/pdb/validation_reports/zf/2zf8 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32036.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Gene: MotY / Plasmid: PTTQ18 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P74944 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.85→54 Å / Num. obs: 10468 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 72.4 Å2 / Rmerge(I) obs: 0.085 | ||||||||||||||||||
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 4 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1490 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.85→41 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1803280.89 / Data cutoff low absF: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.0161 Å2 / ksol: 0.3062 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.85→41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→3.03 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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