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- PDB-1tqg: CheA phosphotransferase domain from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1tqg
TitleCheA phosphotransferase domain from Thermotoga maritima
ComponentsChemotaxis protein cheA
KeywordsTRANSFERASE / HISTIDINE KINASE / PHOSPHOTRANSFER / SIGNAL TRANSDUCTION / CHEMOTAXIS
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / chemotaxis / protein domain specific binding / ATP binding / cytoplasm
Similarity search - Function
Chemotaxis protein CheA, P2 response regulator-binding / Chemotaxis protein CheA, P2 response regulator-binding domain superfamily / P2 response regulator binding domain / HPT domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / : ...Chemotaxis protein CheA, P2 response regulator-binding / Chemotaxis protein CheA, P2 response regulator-binding domain superfamily / P2 response regulator binding domain / HPT domain / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / : / CheW-like domain profile. / CheW-like domain / CheW-like domain superfamily / CheW-like domain / Two component signalling adaptor domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chemotaxis protein CheA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR/MAD PHAING / Resolution: 0.98 Å
AuthorsQuezada, C.M. / Gradinaru, C. / Simon, M.I. / Bilwes, A.M. / Crane, B.R.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Helical Shifts Generate Two Distinct Conformers in the Atomic Resolution Structure of the CheA Phosphotransferase Domain from Thermotoga maritima.
Authors: Quezada, C.M. / Gradinaru, C. / Simon, M.I. / Bilwes, A.M. / Crane, B.R.
History
DepositionJun 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chemotaxis protein cheA


Theoretical massNumber of molelcules
Total (without water)11,8671
Polymers11,8671
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.381, 37.419, 87.542
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-1079-

HOH

21A-1083-

HOH

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Components

#1: Protein Chemotaxis protein cheA


Mass: 11866.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET28a+ / 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.63 Å3/Da / Density % sol: 24.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 28% PEG 8K, 0.1M NaOAc pH=4.5, and 0.2M NH4OAc, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91612 / Wavelength: 0.91612 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91612 Å / Relative weight: 1
ReflectionResolution: 0.98→15 Å / Num. all: 51414 / Num. obs: 51414 / % possible obs: 97.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
PHASESphasing
CNSrefinement
SHELXmodel building
DENZOdata reduction
CNSphasing
SHELXphasing
RefinementMethod to determine structure: MIR/MAD PHAING / Resolution: 0.98→15 Å / Num. parameters: 11406 / Num. restraintsaints: 17322 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 2563 5 %RANDOM
Rwork0.1794 ---
all0.18 51414 --
obs0.1794 51414 97.8 %-
Refine analyzeNum. disordered residues: 48 / Occupancy sum hydrogen: 818 / Occupancy sum non hydrogen: 969.5
Refinement stepCycle: LAST / Resolution: 0.98→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 0 146 2393
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0223
X-RAY DIFFRACTIONs_zero_chiral_vol0.105
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.086
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.05
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.059
X-RAY DIFFRACTIONs_approx_iso_adps0.104

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