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Yorodumi- PDB-2qhk: Crystal structure of methyl-accepting chemotaxis protein from Vib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qhk | ||||||
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Title | Crystal structure of methyl-accepting chemotaxis protein from Vibrio parahaemolyticus RIMD 2210633 | ||||||
Components | Methyl-accepting chemotaxis proteinMethyl-accepting chemotaxis proteins | ||||||
Keywords | SIGNALING PROTEIN / The methyl-accepting chemotaxis protein / Vibrio parahaemolyticus RIMD 2210633 / Structural genomics / PSI-2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio parahaemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å | ||||||
Authors | Zhang, R. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of the methyl-accepting chemotaxis protein from Vibrio parahaemolyticus RIMD 2210633. Authors: Zhang, R. / Li, H. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qhk.cif.gz | 45.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qhk.ent.gz | 35.3 KB | Display | PDB format |
PDBx/mmJSON format | 2qhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/2qhk ftp://data.pdbj.org/pub/pdb/validation_reports/qh/2qhk | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The second part of the biological assembly is generated by the operation 1/2-y,1/2-x,1/2-z |
-Components
#1: Protein | Mass: 19983.787 Da / Num. of mol.: 1 / Fragment: Residues 31-203 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: GI:28896957, VP0183 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q87T87 |
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#2: Chemical | ChemComp-GOL / |
#3: 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: 2.47 Å3/Da / Density % sol: 50.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Bis-Tris, 28% PEG MME 2000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→79.31 Å / Num. all: 15122 / Num. obs: 15013 / % possible obs: 99.28 % / Observed criterion σ(I): 2 / Redundancy: 18.5 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.9→1.957 Å / Redundancy: 17 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 5 / Num. unique all: 1152 / % possible all: 0.934 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.91→79.31 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.198 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.132 / ESU R Free: 0.128 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 34.312 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.91→79.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.96 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 38.361 Å / Origin y: 36.384 Å / Origin z: 15.058 Å
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Refinement TLS group |
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