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- PDB-1xw6: 1.9 angstrom resolution structure of human glutathione S-transfer... -

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Basic information

Entry
Database: PDB / ID: 1xw6
Title1.9 angstrom resolution structure of human glutathione S-transferase M1A-1A complexed with glutathione
ComponentsGlutathione S-transferase Mu 1
KeywordsTRANSFERASE / GLUTATHIONE / CONJUGATION / DETOXIFICATION / CYTOSOLIC / DIMER / ACTIVE SITE
Function / homology
Function and homology information


nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione binding / glutathione derivative biosynthetic process / Glutathione conjugation / Paracetamol ADME / Azathioprine ADME / prostaglandin metabolic process / intercellular bridge ...nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione binding / glutathione derivative biosynthetic process / Glutathione conjugation / Paracetamol ADME / Azathioprine ADME / prostaglandin metabolic process / intercellular bridge / glutathione transferase / glutathione transferase activity / xenobiotic catabolic process / glutathione metabolic process / enzyme binding / protein homodimerization activity / cytosol / cytoplasm
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 / Soluble glutathione S-transferase N-terminal domain profile. / 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 / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Glutathione S-transferase Mu 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPatskovsky, Y. / Patskovska, L. / Almo, S.C. / Listowsky, I.
Citation
Journal: Biochemistry / Year: 2006
Title: Transition state model and mechanism of nucleophilic aromatic substitution reactions catalyzed by human glutathione S-transferase M1a-1a.
Authors: Patskovsky, Y. / Patskovska, L. / Almo, S.C. / Listowsky, I.
#1: Journal: BIOCHEMISTRY / Year: 1999
Title: Function of His107 in the catalytic mechanism of human glutathione S-transferase HGSTM1A-1A
Authors: Patskovsky, Y.V. / Patskovska, L.N. / Listowsky, I.
History
DepositionOct 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase Mu 1
B: Glutathione S-transferase Mu 1
C: Glutathione S-transferase Mu 1
D: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2178
Polymers102,9874
Non-polymers1,2294
Water12,971720
1
A: Glutathione S-transferase Mu 1
B: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1084
Polymers51,4942
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-16 kcal/mol
Surface area19010 Å2
MethodPISA
2
C: Glutathione S-transferase Mu 1
D: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1084
Polymers51,4942
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-16 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.970, 84.380, 212.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological assembly is a homodimer, the asymmetric unit contains two homodimers

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Components

#1: Protein
Glutathione S-transferase Mu 1 / / GSTM1-1 / GST class-mu 1 / GSTM1a-1a / GSTM1b-1b / HB subunit 4 / GTH4


Mass: 25746.842 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTM1, GST1 / Plasmid: pET3A-hGSTM1a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09488, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 720 / 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: 2.4 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 280 K / Method: vapor diffusion / pH: 6.5
Details: 20% PEG4000, pH 6.50, VAPOR DIFFUSION, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 20, 2001 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 80368 / Num. obs: 78917 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.071 / Net I/σ(I): 7.7
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.1 / Num. unique all: 12156 / Rsym value: 0.37 / % possible all: 92.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CCP4model building
CNS1refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GTU

1gtu


Resolution: 1.9→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2353 3.1 %RANDOM
Rwork0.227 ---
all0.24 78917 --
obs0.227 77082 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.9486 Å2 / ksol: 0.313672 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.05 Å20 Å20 Å2
2--2.21 Å20 Å2
3----7.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7216 0 80 720 8016
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_mcbond_it2.112
X-RAY DIFFRACTIONc_mcangle_it3.553.5
X-RAY DIFFRACTIONc_scbond_it3.023
X-RAY DIFFRACTIONc_scangle_it5.115
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 327 2.9 %
Rwork0.351 10899 -
obs-10899 85.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3GSHPARAM.PEPGSHTOP.PEP

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