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Yorodumi- PDB-3lic: Crystal Structure of the extracellular domain of the putative his... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lic | ||||||
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Title | Crystal Structure of the extracellular domain of the putative histidine kinase soHK1S-Z6 | ||||||
Components | Sensor protein | ||||||
Keywords | SIGNALING PROTEIN / PDC fold / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Transferase / Transmembrane / Two-component regulatory system | ||||||
Function / homology | Function and homology information histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 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 | 3lic.cif.gz | 65.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lic.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 3lic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/3lic ftp://data.pdbj.org/pub/pdb/validation_reports/li/3lic | HTTPS FTP |
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-Related structure data
Related structure data | 3li8C 3li9C 3liaC 3libC 3lidC 3lieC 3lifC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30642.025 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 36-308) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: SO_0859 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EII0 |
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#2: Chemical | ChemComp-EDO / |
#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: 2.7 Å3/Da / Density % sol: 54.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.8 Details: 5% PEG3350, 0.5M NH4SO4, 0.1M Na Citrate pH 5.8, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97927, 0.97937, 0.96789 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Redundancy: 6.9 % / Av σ(I) over netI: 28.58 / Number: 196577 / Rmerge(I) obs: 0.068 / Χ2: 1.01 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 28506 / % possible obs: 100 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.3→50 Å / Num. obs: 28506 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.068 / Χ2: 1.013 / Net I/σ(I): 15.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→38.41 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.043 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.279 / ESU R Free: 0.229 / 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: 74.1 Å2 / Biso mean: 27.186 Å2 / Biso min: 2.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→38.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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