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- PDB-4gtu: LIGAND-FREE HOMODIMERIC HUMAN GLUTATHIONE S-TRANSFERASE M4-4 -

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Basic information

Entry
Database: PDB / ID: 4gtu
TitleLIGAND-FREE HOMODIMERIC HUMAN GLUTATHIONE S-TRANSFERASE M4-4
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / GLUTATHIONE / CONJUGATION / DETOXIFICATION / CYTOSOLIC / HOMODIMER
Function / homology
Function and homology information


Biosynthesis of maresin conjugates in tissue regeneration (MCTR) / leukotriene-C4 synthase / leukotriene-C4 synthase activity / nitrobenzene metabolic process / glutathione binding / Glutathione conjugation / long-chain fatty acid biosynthetic process / glutathione transferase / glutathione transferase activity / xenobiotic catabolic process ...Biosynthesis of maresin conjugates in tissue regeneration (MCTR) / leukotriene-C4 synthase / leukotriene-C4 synthase activity / nitrobenzene metabolic process / glutathione binding / Glutathione conjugation / long-chain fatty acid biosynthetic process / glutathione transferase / glutathione transferase activity / xenobiotic catabolic process / intercellular bridge / glutathione metabolic process / enzyme binding / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / : / 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 ...Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / : / 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 S-transferase Mu 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsPatskovsky, Y.V. / Patskovska, L.N. / Listowsky, I.
Citation
Journal: Biochemistry / Year: 1999
Title: An asparagine-phenylalanine substitution accounts for catalytic differences between hGSTM3-3 and other human class mu glutathione S-transferases.
Authors: Patskovsky, Y.V. / Patskovska, L.N. / Listowsky, I.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Isolation and Analysis of the Gene and cDNA for a Human MU Class Glutathione S- Transferase, GSTM4
Authors: Comstock, K.E. / Johnson, K.J. / Rifenbery, D. / Henner, W.D.
History
DepositionMay 12, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2012Group: Other
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Sep 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE
C: GLUTATHIONE S-TRANSFERASE
D: GLUTATHIONE S-TRANSFERASE
E: GLUTATHIONE S-TRANSFERASE
F: GLUTATHIONE S-TRANSFERASE
G: GLUTATHIONE S-TRANSFERASE
H: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)203,6978
Polymers203,6978
Non-polymers00
Water00
1
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)50,9242
Polymers50,9242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: GLUTATHIONE S-TRANSFERASE
D: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)50,9242
Polymers50,9242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: GLUTATHIONE S-TRANSFERASE
F: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)50,9242
Polymers50,9242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: GLUTATHIONE S-TRANSFERASE
H: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)50,9242
Polymers50,9242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.000, 215.700, 94.560
Angle α, β, γ (deg.)90.00, 97.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.849721, -0.214994, -0.481407), (-0.216414, -0.974842, 0.053372), (-0.48077, 0.058832, -0.874871)13.1536, 148.103, -16.4444
2given(0.104001, -0.026619, -0.994221), (0.02066, 0.999484, -0.024599), (0.994363, -0.017982, 0.104497)-20.1361, -53.4721, 27.0213
3given(-0.39954, -0.214856, -0.891181), (0.010513, -0.973156, 0.229906), (-0.916655, 0.082487, 0.391074)-7.4997, 206.811, -32.7277
4given(0.887466, -0.001526, -0.460871), (-0.000426, -0.999997, 0.00249), (-0.460874, -0.002013, -0.887464)-43.9706, 159.7578, 63.2218
5given(0.980887, 0.191516, 0.034389), (-0.192404, 0.981005, 0.024675), (-0.02901, -0.03082, 0.999104)-87.1257, 5.4573, -43.1679
6given(-0.395241, -0.033871, -0.917953), (0.013607, -0.999426, 0.031019), (-0.918477, -0.000231, 0.395475)39.7101, 211.4617, 23.0362
7given(0.10481, 0.166739, -0.980415), (0.021406, 0.985238, 0.169847), (0.994262, -0.038789, 0.099693)-7.026, -64.5572

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Components

#1: Protein
GLUTATHIONE S-TRANSFERASE


Mass: 25462.164 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: LIGAND-FREE, HOMODIMER / Source: (gene. exp.) Homo sapiens (human)
Description: THE GSTM4 CDNA WAS AMPLIFIED USING RT-PCR AND CLONED INTO A PET3A EXPRESSION VECTOR. SYNTHETIC GENE
Cell line: HEPG2 / Cellular location: CYTOPLASM / Gene: GSTM4 / Plasmid: PET3A-GSTM4 / Species (production host): Escherichia coli / Gene (production host): GSTM4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03013, glutathione transferase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 50 %
Crystal growpH: 5.6
Details: 22% PEG4000, 0.1M NA CITRATE,0.2M AMMONIUM ACETATE, PH5.6
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Aug 1, 1997
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→39.4 Å / Num. obs: 30754 / % possible obs: 76.2 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.165 / Rsym value: 0.163
Reflection shellResolution: 3→3.5 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.57 / Rsym value: 0.36 / % possible all: 68.4

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GTU

1gtu


Resolution: 3.3→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.315 2392 10.27 %RANDOM
Rwork0.245 ---
obs-23295 79.5 %-
Refine analyzeLuzzati coordinate error obs: 0.47 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 3.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14352 0 0 0 14352
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.279
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.36
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.222
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.891.5
X-RAY DIFFRACTIONx_mcangle_it3.982
X-RAY DIFFRACTIONx_scbond_it3.572
X-RAY DIFFRACTIONx_scangle_it4.732.5
LS refinement shellResolution: 3.3→3.44 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.322 218 11.7 %
Rwork0.277 1649 -
obs--51.8 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO

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