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Yorodumi- PDB-3wit: Crystal structure of the C-terminal region of VgrG1 from E. coli ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wit | ||||||
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Title | Crystal structure of the C-terminal region of VgrG1 from E. coli O157 EDL933 | ||||||
Components | Putative Vgr protein | ||||||
Keywords | STRUCTURAL PROTEIN / Triple-stranded beta-helix / All beta proteins / Type 6 secretion system component | ||||||
Function / homology | Function and homology information Glycosyl hydrolase fold - #20 / Glycosyl hydrolase fold / Type VI secretion system, RhsGE-associated Vgr family subset / Type VI secretion system, RhsGE-associated Vgr protein / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / Single Sheet / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Uchida, K. / Leiman, P.G. / Arisaka, F. / Kanamaru, S. | ||||||
Citation | Journal: J.Biochem. / Year: 2014 Title: Structure and properties of the C-terminal beta-helical domain of VgrG protein from Escherichia coli O157 Authors: Uchida, K. / Leiman, P.G. / Arisaka, F. / Kanamaru, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wit.cif.gz | 33.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wit.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 3wit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/3wit ftp://data.pdbj.org/pub/pdb/validation_reports/wi/3wit | HTTPS FTP |
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-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: 8618.481 Da / Num. of mol.: 1 / Fragment: UNP residues 561-633 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: ECs0607, VgrG1, Z0707 / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): B384(DE3) / References: UniProt: Q8XBY5 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 35%(v/v) ethanol, 100mM Tris pH8.5, 50mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 9, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→41.84 Å / Num. all: 7237 / Num. obs: 7223 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 18.3 % / Biso Wilson estimate: 32.45 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 43.1 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 15.2 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 7.5 / Num. unique all: 1026 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.95→33.191 Å / SU ML: 0.15 / Isotropic thermal model: Isotropic / σ(F): 0.08 / Phase error: 26.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→33.191 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.4547 Å
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Refinement TLS params. | Method: refined / Origin x: 20.2795 Å / Origin y: 20.1684 Å / Origin z: 85.2587 Å
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Refinement TLS group | Selection details: all |