+Open data
-Basic information
Entry | Database: PDB / ID: 3tmy | ||||||
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Title | CHEY FROM THERMOTOGA MARITIMA (MN-III) | ||||||
Components | CHEY PROTEIN | ||||||
Keywords | CHEMOTAXIS / PHOSPHORYL TRANSFER / SIGNAL TRANSDUCTION / MANGANESE BINDING | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 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.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 | 3tmy.cif.gz | 58.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tmy.ent.gz | 42.7 KB | Display | PDB format |
PDBx/mmJSON format | 3tmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tmy_validation.pdf.gz | 430.7 KB | Display | wwPDB validaton report |
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Full document | 3tmy_full_validation.pdf.gz | 441.6 KB | Display | |
Data in XML | 3tmy_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 3tmy_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/3tmy ftp://data.pdbj.org/pub/pdb/validation_reports/tm/3tmy | HTTPS FTP |
-Related structure data
Related structure data | 1tmySC 2tmyC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.940939, 0.168462, -0.293692), Vector: |
-Components
#1: Protein | Mass: 13234.754 Da / Num. of mol.: 2 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 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.3 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 0.2M AMMONIUM SULFATE, 0.1M HEPES BUFFER (PH 7.0), 25% PEG 4000, 15MM MANGANESE CHLORIDE | ||||||||||||||||||||||||||||||
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: Sep 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: 2.2→20 Å / Num. obs: 12436 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.2→2.37 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 2.5 / % possible all: 94 |
Reflection shell | *PLUS % possible obs: 94 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TMY Resolution: 2.2→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: 576 Å2 / ksol: 1.03 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.021 / Weight: 5 |