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- PDB-7esg: Crystal structure of Haloarcula marismortui CheB with Glutathione... -

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Basic information

Entry
Database: PDB / ID: 7esg
TitleCrystal structure of Haloarcula marismortui CheB with Glutathione S-transferase expression tag
ComponentsGlutathione S-transferase,Protein-glutamate methylesterase/protein-glutamine glutaminase
KeywordsTRANSFERASE / HYDROLASE / CheB methylesterase
Function / homology
Function and homology information


protein-glutamate methylesterase / protein-glutamate methylesterase activity / protein deamination / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein demethylation / phosphorelay response regulator activity / glutathione transferase / glutathione transferase activity / chemotaxis / cytoplasm
Similarity search - Function
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. / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Response regulator receiver 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. / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
Glutathione S-transferase class-mu 26 kDa isozyme / Protein-glutamate methylesterase/protein-glutamine glutaminase
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
Haloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsChen, K.L. / Yang, C.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Haloarcula marismortui CheB with Glutathione S-transferase expression tag
Authors: Chen, K.L. / Yang, C.S.
History
DepositionMay 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase,Protein-glutamate methylesterase/protein-glutamine glutaminase


Theoretical massNumber of molelcules
Total (without water)65,4121
Polymers65,4121
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.058, 93.910, 93.632
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glutathione S-transferase,Protein-glutamate methylesterase/protein-glutamine glutaminase


Mass: 65411.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata), (gene. exp.) Haloarcula marismortui (Halophile)
Gene: cheB / Production host: Escherichia coli (E. coli) / References: UniProt: P08515, UniProt: Q5V0B3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.95 Å3/Da / Density % sol: 36.96 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 200 mM Potassium citrate tribasic monohydrate, pH 8.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.53→30 Å / Num. obs: 17534 / % possible obs: 99.51 % / Redundancy: 6.9 % / Biso Wilson estimate: 35.29 Å2 / Rrim(I) all: 0.097 / Net I/σ(I): 18.5
Reflection shellResolution: 2.53→2.62 Å / Num. unique obs: 1638 / Rrim(I) all: 0.443

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
PHENIX1.19.2_4158model building
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: robetta model

Resolution: 2.53→23.86 Å / Cross valid method: FREE R-VALUE / σ(F): 38.73 / Phase error: 39.0117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3716 1761 10.04 %
Rwork0.3494 15771 -
obs0.3606 17532 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.57 Å2
Refinement stepCycle: LAST / Resolution: 2.53→23.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 0 39 4553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00344585
X-RAY DIFFRACTIONf_angle_d0.8346193
X-RAY DIFFRACTIONf_chiral_restr0.0465701
X-RAY DIFFRACTIONf_plane_restr0.0076810
X-RAY DIFFRACTIONf_dihedral_angle_d8.2366630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.60.40431230.46061119X-RAY DIFFRACTION84.84
2.6-2.680.50561360.42491199X-RAY DIFFRACTION89.68
2.68-2.760.39241320.41571213X-RAY DIFFRACTION90.19
2.76-2.860.4371310.43111172X-RAY DIFFRACTION89.95
2.86-2.980.45051360.39491208X-RAY DIFFRACTION89.88
2.98-3.110.3671340.36871211X-RAY DIFFRACTION90.04
3.11-3.270.34171320.3441199X-RAY DIFFRACTION90.08
3.27-3.480.34371370.35071220X-RAY DIFFRACTION89.9
3.48-3.750.3281330.32761216X-RAY DIFFRACTION90.14
3.75-4.120.29331380.32451229X-RAY DIFFRACTION89.9
4.12-4.710.33261410.31021226X-RAY DIFFRACTION89.69
4.72-5.920.44791370.33311250X-RAY DIFFRACTION90.12
5.93-23.860.44911430.39061317X-RAY DIFFRACTION89.78

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