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Yorodumi- PDB-3lib: Crystal Structure of the extracellular domain of the putative his... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lib | ||||||
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Title | Crystal Structure of the extracellular domain of the putative histidine kinase mmHK1S-Z3 | ||||||
Components | Hypothetical sensory transduction histidine kinase | ||||||
Keywords | SIGNALING PROTEIN / PDC fold | ||||||
Function / homology | Function and homology information protein histidine kinase activity / histidine kinase / membrane => GO:0016020 / signal transduction Similarity search - Function | ||||||
Biological species | Methanosarcina mazei (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.99 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 | 3lib.cif.gz | 513 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lib.ent.gz | 421.7 KB | Display | PDB format |
PDBx/mmJSON format | 3lib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/3lib ftp://data.pdbj.org/pub/pdb/validation_reports/li/3lib | HTTPS FTP |
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-Related structure data
Related structure data | 3li8C 3li9C 3liaC 3licC 3lidC 3lieC 3lifC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 32477.061 Da / Num. of mol.: 10 / Fragment: extracellular domain (UNP residues 32-312) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: DSM 3647 / Gene: MM_2965 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PSW1 #2: Chemical | ChemComp-K / #3: 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: 3.02 Å3/Da / Density % sol: 59.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.7 Details: 2M Na/K phosphate pH6.7, 0.2M NaCl, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.96788 Å | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Detector: CCD | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96788 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 76489 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.9 | ||||||||||||||||||||||||||||||||||||||||||||
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: 2.99→46.72 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 1 / SU B: 18.138 / SU ML: 0.336 / Cross valid method: THROUGHOUT / ESU R Free: 0.449 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.402 Å2
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Refinement step | Cycle: LAST / Resolution: 2.99→46.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.993→3.071 Å / Total num. of bins used: 20
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