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Yorodumi- PDB-3cyp: The crystal structure of the C-terminal domain of Helicobacter py... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cyp | ||||||
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Title | The crystal structure of the C-terminal domain of Helicobacter pylori MotB (residues 125-256). | ||||||
Components | Chemotaxis protein motB | ||||||
Keywords | MEMBRANE PROTEIN / Helicobacter pylori / bacterial flagellar motor / peptidoglycan binding / Bacterial flagellum / Chemotaxis / Flagellar rotation / Inner membrane / Membrane / Transmembrane | ||||||
Function / homology | Function and homology information archaeal or bacterial-type flagellum-dependent cell motility / chemotaxis / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å | ||||||
Authors | Roujeinikova, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Crystal structure of the cell wall anchor domain of MotB, a stator component of the bacterial flagellar motor: implications for peptidoglycan recognition. Authors: Roujeinikova, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cyp.cif.gz | 131 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cyp.ent.gz | 103.3 KB | Display | PDB format |
PDBx/mmJSON format | 3cyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cyp_validation.pdf.gz | 450.4 KB | Display | wwPDB validaton report |
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Full document | 3cyp_full_validation.pdf.gz | 458.6 KB | Display | |
Data in XML | 3cyp_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 3cyp_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/3cyp ftp://data.pdbj.org/pub/pdb/validation_reports/cy/3cyp | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 15939.984 Da / Num. of mol.: 4 / Fragment: C-terminal domain, UNP residues 126-257 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: motB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P56427 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 100 mM Tris/HCl, 16-18% PEG 3350, 200 mM sodium tartrate, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 13, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→61.2 Å / Num. obs: 71913 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 5.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 1.6→50.572 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.932 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.1 / 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 mean: 17.895 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50.572 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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