+Open data
-Basic information
Entry | Database: PDB / ID: 2tmy | ||||||
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Title | CHEY FROM THERMOTOGA MARITIMA (APO-II) | ||||||
Components | CHEY PROTEIN | ||||||
Keywords | CHEMOTAXIS / PHOSPHORYL TRANSFER / SIGNAL TRANSDUCTION | ||||||
Function / homology | Function and homology information archaeal or bacterial-type flagellum-dependent cell motility / phosphorelay signal transduction system / chemotaxis / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Usher, K.C. / De La Cruz, A. / Dahlquist, F.W. / Remington, S.J. | ||||||
Citation | Journal: Protein Sci. / Year: 1998 Title: Crystal structures of CheY from Thermotoga maritima do not support conventional explanations for the structural basis of enhanced thermostability. Authors: Usher, K.C. / de la Cruz, A.F. / Dahlquist, F.W. / Swanson, R.V. / Simon, M.I. / Remington, S.J. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Magnesium Binding to the Bacterial Chemotaxis Protein Chey Results in Large Conformational Changes Involving its Functional Surface Authors: Bellsolell, L. / Prieto, J. / Serrano, L. / Coll, M. #2: Journal: J.Mol.Biol. / Year: 1994 Title: Erratum. Magnesium Binding to the Bacterial Chemotaxis Protein Chey Results in Large Conformational Changes Involving its Functional Surface Authors: Bellsolell, L. / Prieto, J. / Serrano, L. / Coll, M. #3: Journal: J.Biol.Chem. / Year: 1991 Title: Crystal Structure of Escherichia Coli Chey Refined at 1.7-A Resolution Authors: Volz, K. / Matsumura, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2tmy.cif.gz | 31 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2tmy.ent.gz | 23.4 KB | Display | PDB format |
PDBx/mmJSON format | 2tmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/2tmy ftp://data.pdbj.org/pub/pdb/validation_reports/tm/2tmy | HTTPS FTP |
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-Related structure data
Related structure data | 1tmySC 3tmyC 4tmyC 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
#1: Protein | Mass: 13234.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Cellular location: CYTOPLASM / Gene: CHEY / Plasmid: PQE12 / Cellular location (production host): CYTOPLASM / Gene (production host): CHEY / Production host: Escherichia coli (E. coli) / Strain (production host): K0641/RECA / References: UniProt: Q56312 |
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#2: 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: 3 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: 0.2M AMMONIUM SULFATE, 0.1M ACETATE BUFFER (PH 4.6), 30% PEG 4000, 15MM MGCL2 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Dec 15, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 6660 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.3→2.6 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 2.5 / % possible all: 76 |
Reflection | *PLUS % possible obs: 82 % / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 76 % |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TMY Resolution: 2.3→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO Details: DISORDERED SIDE-CHAINS WERE MODELED STEREOCHEMICALLY AND HAVE THEIR OCCUPANCY SET ARBITRARILY TO 0.0.
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 863 Å2 / ksol: 1.21 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.015 / Weight: 2 |