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Yorodumi- PDB-3li8: Crystal Structure of the extracellular domain of the putative his... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3li8 | ||||||
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Title | Crystal Structure of the extracellular domain of the putative histidine kinase mmHK1S-Z2 | ||||||
Components | Hypothetical sensory transduction histidine kinase | ||||||
Keywords | SIGNALING PROTEIN / PDC fold | ||||||
Function / homology | Function and homology information protein histidine kinase activity / histidine kinase / signal transduction / plasma membrane Similarity search - Function | ||||||
Biological species | Methanosarcina mazei (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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 | 3li8.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3li8.ent.gz | 53.1 KB | Display | PDB format |
PDBx/mmJSON format | 3li8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/3li8 ftp://data.pdbj.org/pub/pdb/validation_reports/li/3li8 | HTTPS FTP |
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-Related structure data
Related structure data | 3li9C 3liaC 3libC 3licC 3lidC 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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Unit cell |
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-Components
#1: Protein | Mass: 33117.594 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 32-313) Source method: isolated from a genetically manipulated source Details: SeMet protein / Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: DSM 3647 / Gene: MM_2955 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PSW8 | ||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | #4: 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: 2.21 Å3/Da / Density % sol: 44.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.6 Details: 15% PEG3350, 0.21M NH4SO4, 0.1M sodium cacodylate, pH 5.6, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.96784 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Detector: CCD / Date: Aug 2, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96784 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→50 Å / Num. obs: 30021 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.094 / Χ2: 1.016 / Net I/σ(I): 13.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→53.45 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.193 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.853 / SU B: 2.177 / SU ML: 0.072 / SU R Cruickshank DPI: 0.115 / SU Rfree: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.118 / 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: 55.7 Å2 / Biso mean: 21.395 Å2 / Biso min: 3.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→53.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.749→1.794 Å / Total num. of bins used: 20
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