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Yorodumi- PDB-3gig: Crystal structure of phosphorylated DesKC in complex with AMP-PCP -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gig | ||||||
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Title | Crystal structure of phosphorylated DesKC in complex with AMP-PCP | ||||||
Components | (Sensor histidine kinase desK) x 2 | ||||||
Keywords | TRANSFERASE / four-helix bundle / GHL ATPase domain / Cell membrane / Kinase / Membrane / Phosphoprotein / Transmembrane / Two-component regulatory system | ||||||
Function / homology | Function and homology information histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / protein dimerization activity / protein kinase activity / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.502 Å | ||||||
Authors | Trajtenberg, F. / Albanesi, D. / Alzari, P.M. / Buschiazzo, A. / de Mendoza, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Structural plasticity and catalysis regulation of a thermosensor histidine kinase Authors: Albanesi, D. / Martin, M. / Trajtenberg, F. / Mansilla, M.C. / Haouz, A. / Alzari, P.M. / de Mendoza, D. / Buschiazzo, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gig.cif.gz | 173 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gig.ent.gz | 135.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/3gig ftp://data.pdbj.org/pub/pdb/validation_reports/gi/3gig | HTTPS FTP |
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-Related structure data
Related structure data | 3ehfSC 3ehhC 3ehjC 3gieC 3gifC 3ehgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 24965.623 Da / Num. of mol.: 1 / Fragment: entire cytoplasmic region Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yocF / Plasmid: pQE32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O34757, histidine kinase | ||
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#2: Protein | Mass: 25044.596 Da / Num. of mol.: 1 / Fragment: entire cytoplasmic region Source method: isolated from a genetically manipulated source Details: phosphorylated entire cytoplasmic region / Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yocF / Plasmid: pQE32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O34757, histidine kinase | ||
#3: Chemical | #4: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 70.71 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: PEG3000, MgCl2, CHES, AMP-PCP, pH 9.5, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 9, 2008 / Details: mirrors |
Radiation | Monochromator: multilayer mirrors (Varimax-HF) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→28.846 Å / Num. all: 11051 / Num. obs: 10993 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 92.42 Å2 / Rmerge(I) obs: 0.047 |
Reflection shell | Resolution: 3.5→3.6 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 4 / Num. measured obs: 3362 / Num. unique all: 864 / Num. unique obs: 864 / % possible all: 99.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EHG and 3EHF Resolution: 3.502→28.846 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: -0 Isotropic thermal model: two factors per residue (main chain + side chain), 5 body TLS model Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 36.28 / Stereochemistry target values: ML Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.815 Å2 / ksol: 0.245 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 427.44 Å2 / Biso mean: 147.188 Å2 / Biso min: 33.98 Å2
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Refinement step | Cycle: LAST / Resolution: 3.502→28.846 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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