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Yorodumi- PDB-1i59: STRUCTURE OF THE HISTIDINE KINASE CHEA ATP-BINDING DOMAIN IN COMP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i59 | ||||||
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Title | STRUCTURE OF THE HISTIDINE KINASE CHEA ATP-BINDING DOMAIN IN COMPLEX WITH ADPNP AND MAGENSIUM | ||||||
Components | CHEMOTAXIS PROTEIN CHEA | ||||||
Keywords | SIGNALING PROTEIN / TRANSFERASE / beta-alpha sandwich | ||||||
Function / homology | Function and homology information histidine kinase / phosphorelay sensor kinase activity / chemotaxis / protein domain specific binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bilwes, A.M. / Quezada, C.M. / Croal, L.R. / Crane, B.R. / Simon, M.I. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Nucleotide binding by the histidine kinase CheA. Authors: Bilwes, A.M. / Quezada, C.M. / Croal, L.R. / Crane, B.R. / Simon, M.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i59.cif.gz | 91.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i59.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 1i59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/1i59 ftp://data.pdbj.org/pub/pdb/validation_reports/i5/1i59 | HTTPS FTP |
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-Related structure data
Related structure data | 1i58C 1i5aC 1i5bC 1i5cC 1i5dC 1b3qS 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21079.270 Da / Num. of mol.: 2 / Fragment: DOMAIN P4 / Mutation: R354H, I353S, K352G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q56310, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor |
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-Non-polymers , 5 types, 248 molecules
#2: Chemical | ChemComp-ACT / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ANP / |
#5: Chemical | ChemComp-ADP / |
#6: 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: 2.01 Å3/Da / Density % sol: 38.88 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 8000 33-36% Ammonium acetate 0.8 M sodium acetate 0.085 M pH 4.5. VAPOR DIFFUSION, HANGING DROP at 293 K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 4.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 10, 2000 |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 27387 / Num. obs: 27387 / % possible obs: 87 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 35 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 6 / % possible all: 42 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 42 % / Mean I/σ(I) obs: 6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B3Q Resolution: 1.8→26.08 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 101404152.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.82 Å2 / ksol: 0.359 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→26.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.22 / Rfactor Rfree: 0.249 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.424 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.375 |