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- PDB-3sft: Crystal structure of Thermotoga maritima CheB methylesterase cata... -

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Basic information

Entry
Database: PDB / ID: 3sft
TitleCrystal structure of Thermotoga maritima CheB methylesterase catalytic domain
ComponentsChemotaxis response regulator protein-glutamate methylesterase
KeywordsHYDROLASE / modified doubly-wound/fold / Methylesterase / chemoreceptor
Function / homology
Function and homology information


protein-glutamate methylesterase / protein-glutamate methylesterase activity / protein-glutamine glutaminase activity / protein-glutamine glutaminase / phosphorelay response regulator activity / chemotaxis / cytoplasm
Similarity search - Function
Methylesterase CheB, C-terminal domain / Signal transduction response regulator, chemotaxis, protein-glutamate methylesterase / Protein-glutamate methylesterase/protein-glutamine glutaminase, CheB type / Methylesterase CheB, C-terminal / CheB methylesterase / CheB-type methylesterase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...Methylesterase CheB, C-terminal domain / Signal transduction response regulator, chemotaxis, protein-glutamate methylesterase / Protein-glutamate methylesterase/protein-glutamine glutaminase, CheB type / Methylesterase CheB, C-terminal / CheB methylesterase / CheB-type methylesterase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein-glutamate methylesterase/protein-glutamine glutaminase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPark, S.Y. / Crane, B.R.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: An insight into the interaction mode between CheB and chemoreceptor from two crystal structures of CheB methylesterase catalytic domain
Authors: Cho, K.H. / Crane, B.R. / Park, S.Y.
History
DepositionJun 14, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Chemotaxis response regulator protein-glutamate methylesterase


Theoretical massNumber of molelcules
Total (without water)20,8951
Polymers20,8951
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.467, 65.075, 78.353
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chemotaxis response regulator protein-glutamate methylesterase / CheB


Mass: 20895.289 Da / Num. of mol.: 1 / Fragment: CheB methylesterase catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: cheB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9WYN9, protein-glutamate methylesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.27 Å3/Da / Density % sol: 62.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M cacodylate, 30%(w/v) PEG 8K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 13555

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CHD

1chd


Resolution: 2.15→30 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.223 -10 %random
Rwork0.203 ---
obs-13555 --
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 0 106 1547

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