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Yorodumi- PDB-3lid: Crystal Structure of the extracellular domain of the putative his... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lid | ||||||
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Title | Crystal Structure of the extracellular domain of the putative histidine kinase vpHK1S-Z8 | ||||||
Components | Putative sensory box/GGDEF family protein | ||||||
Keywords | SIGNALING PROTEIN / PDC fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio parahaemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.76 Å | ||||||
Authors | Zhang, Z. / Hendrickson, W.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Structural characterization of the predominant family of histidine kinase sensor domains. Authors: Zhang, Z. / Hendrickson, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lid.cif.gz | 141.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lid.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 3lid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/3lid ftp://data.pdbj.org/pub/pdb/validation_reports/li/3lid | HTTPS FTP |
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-Related structure data
Related structure data | 3li8C 3li9C 3liaC 3libC 3licC 3lieC 3lifC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 34255.449 Da / Num. of mol.: 2 / Fragment: extracellular domain (UNP residues 28-313) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: VP0354 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87SR8 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: 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: 2.65 Å3/Da / Density % sol: 53.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.2 Details: 5% PEG8K, 0.2M NaCl, 0.1M Na/K Phosphate pH6.2, vapor diffusion, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation |
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Radiation wavelength |
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Reflection | Redundancy: 6.3 % / Av σ(I) over netI: 33.54 / Number: 581055 / Rmerge(I) obs: 0.102 / Χ2: 1.02 / D res high: 2.01 Å / D res low: 50 Å / Num. obs: 92883 / % possible obs: 99.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.76→50 Å / Num. obs: 72469 / % possible obs: 99 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.054 / Χ2: 1.004 / Net I/σ(I): 18.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.76→37.807 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.961 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.94 Å2 / Biso mean: 24.942 Å2 / Biso min: 11.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→37.807 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.756→1.802 Å / Total num. of bins used: 20
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