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- PDB-7miq: Crystal structure of a Glutathione S-transferase class Gtt2 of Vi... -

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Basic information

Entry
Database: PDB / ID: 7miq
TitleCrystal structure of a Glutathione S-transferase class Gtt2 of Vibrio parahaemolyticus (VpGSTT2)
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / GST folding / thioredoxin domain / Gtt2 class
Function / homology
Function and homology information


glutathione metabolic process / transferase activity
Similarity search - Function
Gtt2-like, C-terminal / Gtt2-like, N-terminal / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / 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 ...Gtt2-like, C-terminal / Gtt2-like, N-terminal / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / 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
DI(HYDROXYETHYL)ETHER / Glutathione S-transferase
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsValenzuela-Chavira, I. / Serrano-Posada, H. / Lopez-Zavala, A.A. / Garcia-Orozco, K.D. / Sotelo-Mundo, R.R.
Funding support Mexico, 3items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)CB-2014-237963 Mexico
Consejo Nacional de Ciencia y Tecnologia (CONACYT)INFR-2014-01-225455 Mexico
Department of Energy (DOE, United States)DE-AC02-76SF00515 Mexico
CitationJournal: Toxins / Year: 2021
Title: A Novel Glutathione S -Transferase Gtt2 Class (VpGSTT2) Is Found in the Genome of the AHPND/EMS Vibrio parahaemolyticus Shrimp Pathogen.
Authors: Valenzuela-Chavira, I. / Corona-Martinez, D.O. / Garcia-Orozco, K.D. / Beltran-Torres, M. / Sanchez-Lopez, F. / Arvizu-Flores, A.A. / Sugich-Miranda, R. / Lopez-Zavala, A.A. / Robles-Zepeda, ...Authors: Valenzuela-Chavira, I. / Corona-Martinez, D.O. / Garcia-Orozco, K.D. / Beltran-Torres, M. / Sanchez-Lopez, F. / Arvizu-Flores, A.A. / Sugich-Miranda, R. / Lopez-Zavala, A.A. / Robles-Zepeda, R.E. / Islas-Osuna, M.A. / Ochoa-Leyva, A. / Toney, M.D. / Serrano-Posada, H. / Sotelo-Mundo, R.R.
History
DepositionApr 17, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionJul 7, 2021ID: 6ED8
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: 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
B: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4695
Polymers48,1602
Non-polymers3083
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, Kd: GSH 257.8 microM / GTS inibitor 57.9 microM
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-26 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.254, 50.411, 69.620
Angle α, β, γ (deg.)90.000, 90.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutathione S-transferase


Mass: 24080.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: C1S91_22750 / Plasmid: pET11a / Details (production host): pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A2R9VI90, glutathione transferase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 39.99 % / Description: bar shaped crystal, 0.15 mm
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 0.1 M Bis-tris buffer pH 6.5, 30% w/v polyethylene glycol 3350
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.181 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.181 Å / Relative weight: 1
ReflectionResolution: 1.92→40.83 Å / Num. obs: 29129 / % possible obs: 98.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 23.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Net I/σ(I): 5.8
Reflection shellResolution: 1.92→2.24 Å / Redundancy: 5 % / Rmerge(I) obs: 0.26 / Num. unique obs: 3971 / CC1/2: 0.943 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIX1.19.1_4122phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ERF

3erf


Resolution: 1.92→40.83 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2083 1403 4.82 %
Rwork0.1628 27718 -
obs0.1649 29121 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.46 Å2 / Biso mean: 29.282 Å2 / Biso min: 9.6 Å2
Refinement stepCycle: final / Resolution: 1.92→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 19 330 3601
Biso mean--36.53 33.64 -
Num. residues----407
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.92-1.990.28441630.2045250689
1.99-2.070.24611330.1814269697
2.07-2.160.22141400.1707280898
2.16-2.280.21211180.1646280898
2.28-2.420.20211600.1653273697
2.42-2.610.21371430.1653277498
2.61-2.870.21591630.1646281699
2.87-3.280.2131130.1612283198
3.28-4.140.18031120.146284298
4.14-40.80.19631580.1632290199

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