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Yorodumi- PDB-9p6i: Crystal Structure of the Histidine Kinase VC2136 from Vibrio chol... -
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Basic information
| Entry | Database: PDB / ID: 9p6i | ||||||
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| Title | Crystal Structure of the Histidine Kinase VC2136 from Vibrio cholerae serotype O1 | ||||||
Components | histidine kinase | ||||||
Keywords | TRANSFERASE / Center for Structural Biology of Infectious Diseases (CSBID) / Histidine kinase / Structural Genomics | ||||||
| Function / homology | Function and homology information | ||||||
| Biological species | Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Wawrzak, Z. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID) | ||||||
| Funding support | United States, 1items
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Citation | Journal: To Be PublishedTitle: Crystal Structure of the Histidine Kinase from Vibrio cholerae serotype O1 Authors: Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Wawrzak, Z. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID) | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9p6i.cif.gz | 583.5 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb9p6i.ent.gz | 481.1 KB | Display | PDB format |
| PDBx/mmJSON format | 9p6i.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9p6i_validation.pdf.gz | 508.5 KB | Display | wwPDB validaton report |
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| Full document | 9p6i_full_validation.pdf.gz | 525.7 KB | Display | |
| Data in XML | 9p6i_validation.xml.gz | 57.6 KB | Display | |
| Data in CIF | 9p6i_validation.cif.gz | 72.4 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/9p6i ftp://data.pdbj.org/pub/pdb/validation_reports/p6/9p6i | HTTPS FTP |
-Related structure data
| Similar structure data | Similarity search - Function & homology F&H Search |
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| Other databases |
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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: 39346.504 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)Gene: VC_2136 / Plasmid: pMCSG53 / Production host: ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | |
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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: 2.6 Å3/Da / Density % sol: 52.7 % |
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| Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein: 6.5 mg/ml, 0.15M Sodium chloride, 0.01M Tris pH 8.3; Screen: Anions (G8), 0.37M Sodium sulfate, 0.1M MES pH 6.5. Cryo: 2M Lithium sulfate. |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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| Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97848 Å |
| Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 17, 2021 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.97848 Å / Relative weight: 1 |
| Reflection | Resolution: 2.75→30 Å / Num. obs: 45970 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 68.8 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.034 / Rsym value: 0.106 / Χ2: 1.136 / Net I/σ(I): 23.9 |
| Reflection shell | Resolution: 2.75→2.8 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2314 / CC1/2: 0.634 / CC star: 0.881 / Rpim(I) all: 0.418 / Χ2: 0.997 / % possible all: 100 |
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Processing
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| Refinement | Method to determine structure: SAD / Resolution: 2.75→28.22 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.901 / SU B: 34.487 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 93.051 Å2
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| Refinement step | Cycle: 1 / Resolution: 2.75→28.22 Å
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About Yorodumi



Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
X-RAY DIFFRACTION
United States, 1items
Citation
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