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Yorodumi- PDB-2ch4: Complex between Bacterial Chemotaxis histidine kinase CheA domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ch4 | ||||||
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Title | Complex between Bacterial Chemotaxis histidine kinase CheA domains P4 and P5 and receptor-adaptor protein CheW | ||||||
Components |
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Keywords | TRANSFERASE/CHEMOTAXIS / CHEMOTAXIS / PROTEIN-PROTEIN COMPLEX / SIGNAL TRANSDUCTION / HISTIDINE KINASE / SENSORY TRANSDUCTION / PHOSPHORYLATION / TRANSFERASE / TRANSFERASE-CHEMOTAXIS complex | ||||||
Function / homology | Function and homology information histidine kinase / phosphorelay sensor kinase activity / chemotaxis / protein domain specific binding / signal transduction / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | THERMOTOGA MARITIMA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Park, S.Y. / Bilwes, A.M. / Crane, B.R. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2006 Title: Reconstruction of the Chemotaxis Receptor-Kinase Assembly Authors: Park, S.Y. / Borbat, P.P. / Gonzalez-Bonet, G. / Bhatnagar, J. / Pollard, A.M. / Freed, J.H. / Bilwes, A.M. / Crane, B.R. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ch4.cif.gz | 191.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ch4.ent.gz | 151.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ch4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ch4_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2ch4_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2ch4_validation.xml.gz | 43.8 KB | Display | |
Data in CIF | 2ch4_validation.cif.gz | 57.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/2ch4 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/2ch4 | HTTPS FTP |
-Related structure data
Related structure data | 2ch7C 1b3qS 1k0sS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35551.121 Da / Num. of mol.: 2 Fragment: CHEA KINASE AND REGULATORY DOMAINS, RESIDUES 355-671 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q56310, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor #2: Protein | Mass: 16977.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q56311 #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | K352G, I353S, R354H MUTATIONS INTRODUCED | |
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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: 5.14 Å3/Da / Density % sol: 76 % |
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Crystal grow | Details: PEG 4K 3-5%,NA ACETATE 0.1M PH 4.5,ADPNP 1MM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 31, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→30 Å / Num. obs: 27869 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 15 % / Biso Wilson estimate: 90 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 40 |
Reflection shell | Resolution: 3.5→3.6 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 10 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1B3Q AND 1K0S Resolution: 3.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE MOST RELEVANT BIOMOLECULE FOR THE CHEA DOMAINS P4-P5-CHEW COMPLEX IS PROBABLY MOL B (352- 672) - MOL Y. IN MOL A, THE ASSOCIATION BETWEEN DOMAINS P4 AND P5 IS PROBABLY AN ARTIFACT DUE TO ...Details: THE MOST RELEVANT BIOMOLECULE FOR THE CHEA DOMAINS P4-P5-CHEW COMPLEX IS PROBABLY MOL B (352- 672) - MOL Y. IN MOL A, THE ASSOCIATION BETWEEN DOMAINS P4 AND P5 IS PROBABLY AN ARTIFACT DUE TO THE USE OF A TRUNCATED CHEA FRAGMENT. CHEA DOMAIN P3 IN PDB ENTRY 1B3Q BINDS P5 WHERE P4 LIES IN MOLA OF THIS ENTRY. DISORDERED REGIONS WERE MODELLED IN POLYGLY OR POLYALA OR OMITTED IN MOL B (B493-B506 MISSING). DOMAIN CHEA-P4 (MOL B RESIDUES 352-540), WHICH IS IN CONTACT WITH A LARGE SOLVENT CHANNEL IS INCREASINGLY DISORDERED AS IT NEARS THE CHANNEL REGION, RESULTING IN VERY HIGH B-FACTORS. REMOVING OR KEEPING THESE REGIONS IN THE REFINEMENT HAS NO IMPACT ON THE R-FACTOR.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 80 Å2 / ksol: 0.242 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 120 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.6 Å
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