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- PDB-5hwl: Human glutathione s-transferase Mu2 complexed with BDEA, monoclin... -

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Basic information

Entry
Database: PDB / ID: 5hwl
TitleHuman glutathione s-transferase Mu2 complexed with BDEA, monoclinic crystal form
ComponentsGlutathione S-transferase Mu 2
KeywordsTRANSFERASE / Inhibitor / Complex / Target
Function / homology
Function and homology information


nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / glutathione binding / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / relaxation of cardiac muscle / intercellular bridge ...nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / glutathione binding / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / relaxation of cardiac muscle / intercellular bridge / positive regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / cellular response to caffeine / glutathione transferase / glutathione transferase activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / xenobiotic catabolic process / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / glutathione metabolic process / sarcoplasmic reticulum / fatty acid binding / signaling receptor binding / enzyme binding / protein homodimerization activity / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, Mu class / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferase, Mu class / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Chem-NNE / Glutathione S-transferase Mu 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhang, X. / Wei, J. / Wu, S. / Zhang, H.P. / Luo, M. / Yang, X.L. / Liao, F. / Wang, D.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81301395 China
CitationJournal: To Be Published
Title: Human glutathione s-transferase Mu2 complexed with BDEA, monoclinic crystal form
Authors: Zhang, X. / Wei, J. / Wu, S. / Zhang, H.P. / Luo, M. / Yang, X.L. / Liao, F. / Wang, D.Q.
History
DepositionJan 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase Mu 2
B: Glutathione S-transferase Mu 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5645
Polymers51,2912
Non-polymers1,2733
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-22 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.970, 48.890, 90.990
Angle α, β, γ (deg.)90.000, 93.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutathione S-transferase Mu 2 / GST class-mu 2 / GSTM2-2


Mass: 25645.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTM2, GST4 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P28161, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-NNE / N,N'-(butane-1,4-diyl)bis{2-[2,3-dichloro-4-(2-methylidenebutanoyl)phenoxy]acetamide}


Mass: 658.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H32Cl4N2O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.21 Å3/Da / Density meas: 4 Mg/m3 / Density % sol: 44.26 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS. Columnar crystal, 0.1mm X 0.1 mm X 0.5 mm
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.02 M Magnesium Chloride, 0.1M HEPES,pH 6.8, polyacrylic acid sodium salt 5100
PH range: 6.0-7.2 / Temp details: 20

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.6→48.89 Å / Num. obs: 414184 / % possible obs: 98.9 % / Redundancy: 7.1 % / Net I/σ(I): 12.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XW5

1xw5


Resolution: 1.6→45.551 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 1943 3.39 %Random
Rwork0.1782 55327 --
obs0.1792 57270 96.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.49 Å2 / Biso mean: 20.4766 Å2 / Biso min: 7.22 Å2
Refinement stepCycle: final / Resolution: 1.6→45.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 82 223 3798
Biso mean--20 25.22 -
Num. residues----433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073747
X-RAY DIFFRACTIONf_angle_d1.0645050
X-RAY DIFFRACTIONf_chiral_restr0.057520
X-RAY DIFFRACTIONf_plane_restr0.006649
X-RAY DIFFRACTIONf_dihedral_angle_d21.4561423
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.28411290.2263758388792
1.64-1.68440.21751390.20663770390993
1.6844-1.73390.24951300.19713798392895
1.7339-1.78990.24171240.2063881400595
1.7899-1.85390.21641440.19773921406596
1.8539-1.92810.21911220.19443945406797
1.9281-2.01590.22151450.19063986413197
2.0159-2.12210.22221460.17864003414998
2.1221-2.25510.21141480.17493966411498
2.2551-2.42920.18691420.17924014415698
2.4292-2.67360.19711340.17964021415598
2.6736-3.06050.21631350.18563983411897
3.0605-3.85550.20371460.163941024248100
3.8555-45.56930.18131590.1624179433899

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