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- PDB-1tmy: CHEY FROM THERMOTOGA MARITIMA (APO-I) -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1tmy
TitleCHEY FROM THERMOTOGA MARITIMA (APO-I)
ComponentsCHEY PROTEIN
KeywordsCHEMOTAXIS / 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
: / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chemotaxis protein CheY
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsUsher, 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
DepositionMay 16, 1997Processing site: BNL
Revision 1.0Nov 19, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHEY PROTEIN


Theoretical massNumber of molelcules
Total (without water)13,2351
Polymers13,2351
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.040, 53.950, 34.160
Angle α, β, γ (deg.)90.00, 95.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CHEY PROTEIN / TMY


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 50 %
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 0.1M TRIS BUFFER (PH 8.5) AND 1.8M AMMONIUM PHOSPHATE
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.1 MTris1reservoir
31.8 Mammonium phosphate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 19, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 7985 / % possible obs: 83 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 5.5
Reflection shellResolution: 1.9→2.25 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 3 / % possible all: 69

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Processing

Software
NameVersionClassification
RSSmodel building
TNT5Erefinement
R-AXISdata reduction
OSCILLdata reduction
R-AXISdata scaling
SCALEdata scaling
RSSphasing
RefinementMethod to determine structure: SIRAS / MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CHY

3chy


Resolution: 1.9→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.
RfactorNum. reflection% reflection
Rwork0.186 --
all-7985 -
obs-7985 83 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 247 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms900 0 0 15 915
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0179131.5
X-RAY DIFFRACTIONt_angle_deg2.612193
X-RAY DIFFRACTIONt_dihedral_angle_d18.565750
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.023242
X-RAY DIFFRACTIONt_gen_planes0.0211275
X-RAY DIFFRACTIONt_it8.619131
X-RAY DIFFRACTIONt_nbd0.0161220
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.560
X-RAY DIFFRACTIONt_planar_d0.0232
X-RAY DIFFRACTIONt_plane_restr0.0215

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