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Yorodumi- PDB-3lif: Crystal Structure of the extracellular domain of the putative his... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lif | ||||||
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Title | Crystal Structure of the extracellular domain of the putative histidine kinase rpHK1S-Z16 | ||||||
Components | Putative diguanylate cyclase (GGDEF) with PAS/PAC domain | ||||||
Keywords | SIGNALING PROTEIN / PDC fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 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 | 3lif.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lif.ent.gz | 88.5 KB | Display | PDB format |
PDBx/mmJSON format | 3lif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/3lif ftp://data.pdbj.org/pub/pdb/validation_reports/li/3lif | HTTPS FTP |
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-Related structure data
Related structure data | 3li8C 3li9C 3liaC 3libC 3licC 3lidC 3lieC 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: 28769.756 Da / Num. of mol.: 2 / Fragment: extracellular domain (UNP residues 40-293) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Gene: RPA3616 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6N3S7 #2: Chemical | #3: Chemical | #4: 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: 4.57 Å3/Da / Density % sol: 73.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.6 Details: 0.2M NH4Ac, 0.1M citrate pH5.6, 30% MPD, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97918, 0.97935, 0.96788 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Redundancy: 12.9 % / Av σ(I) over netI: 43.17 / Number: 725323 / Rmerge(I) obs: 0.065 / Χ2: 1 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 56039 / % possible obs: 100 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.7→50 Å / Num. obs: 56039 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.065 / Χ2: 0.996 / Net I/σ(I): 12.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→42.39 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.893 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.23 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.316 / ESU R Free: 0.262 / 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: 103.57 Å2 / Biso mean: 41.753 Å2 / Biso min: 2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→42.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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