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Yorodumi- PDB-3d36: How to Switch Off a Histidine Kinase: Crystal Structure of Geobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d36 | ||||||
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Title | How to Switch Off a Histidine Kinase: Crystal Structure of Geobacillus stearothermophilus KinB with the Inhibitor Sda | ||||||
Components | (Sporulation kinase ...) x 2 | ||||||
Keywords | Transferase/Transferase inhibitor / GHKL ATPase / Four Helix Bundle / Class I Two-Component Histidine Kinase / Kinase / Phosphoprotein / Transferase / Two-component regulatory system / Transferase-Transferase inhibitor COMPLEX | ||||||
Function / homology | Function and homology information Sporulation inhibitor A / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.03 Å | ||||||
Authors | Bick, M.J. / Lamour, V. / Rajashankar, K.R. / Gordiyenko, Y. / Robinson, C.V. / Darst, S.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: How to switch off a histidine kinase: crystal structure of Geobacillus stearothermophilus KinB with the inhibitor Sda Authors: Bick, M.J. / Lamour, V. / Rajashankar, K.R. / Gordiyenko, Y. / Robinson, C.V. / Darst, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d36.cif.gz | 117.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d36.ent.gz | 89.8 KB | Display | PDB format |
PDBx/mmJSON format | 3d36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d36_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3d36_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3d36_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 3d36_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/3d36 ftp://data.pdbj.org/pub/pdb/validation_reports/d3/3d36 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Sporulation kinase ... , 2 types, 3 molecules ABC
#1: Protein | Mass: 27011.338 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Strain: 10 / Gene: GK1832, GKA09 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: histidine kinase #2: Protein/peptide | | Mass: 5496.421 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Strain: 10 / Gene: GK2527 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) |
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-Non-polymers , 4 types, 381 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MPD / ( #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | AUTHORS STATE THAT THE SEQUENCE WAS OBTAINED FROM THE UNIVERSITY OF OKLAHOMA UNFINISHED GEOBACILLUS ...AUTHORS STATE THAT THE SEQUENCE WAS OBTAINED FROM THE UNIVERSITY |
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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: 3.34 Å3/Da / Density % sol: 63.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 40% 2-methyl-2,4-pentanediol, 0.2M lithium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2006 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→50 Å / Num. all: 53462 / Num. obs: 52393 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 2.03→2.1 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.43 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.03→42.41 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.179 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.13 / Stereochemistry target values: Engh & Huber
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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: 40.502 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→42.41 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.03 Å / Num. reflection Rwork: 3617 / Num. reflection all: 3837 / Total num. of bins used: 20 |