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- PDB-1xwk: 2.3 angstrom resolution crystal structure of human glutathione S-... -

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Basic information

Entry
Database: PDB / ID: 1xwk
Title2.3 angstrom resolution crystal structure of human glutathione S-transferase M1A-1A complexed with glutathionyl-S-dinitrobenzene
ComponentsGlutathione S-transferase Mu 1
KeywordsTRANSFERASE / GLUTATHIONE / CONJUGATION / DETOXIFICATION / CYTOSOLIC / DIMER / ACTIVE SITE / GLUTATHIONYL-S-DINITROBENZENE / GS-DNB / 1-CHLORO-2 / 4-DINITROBENZENE / CDNB
Function / homology
Function and homology information


nitrobenzene metabolic process / cellular detoxification of nitrogen compound / glutathione derivative biosynthetic process / glutathione binding / hepoxilin biosynthetic process / Glutathione conjugation / Paracetamol ADME / Azathioprine ADME / prostaglandin metabolic process / intercellular bridge ...nitrobenzene metabolic process / cellular detoxification of nitrogen compound / glutathione derivative biosynthetic process / glutathione binding / hepoxilin 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 / 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 / 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 S-(2,4 DINITROBENZENE) / Glutathione S-transferase Mu 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Functions of His-107 in the Catalytic Mechanism of Human Glutathione S-Transferase Hgstm1A-1A
Authors: Patskovsky, Y.V. / Patskovska, L.N. / Listowsky, I.
History
DepositionNov 1, 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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6616
Polymers77,2413
Non-polymers1,4203
Water2,864159
1
A: Glutathione S-transferase Mu 1
C: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4414
Polymers51,4942
Non-polymers9472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-28 kcal/mol
Surface area18570 Å2
MethodPISA
2
B: Glutathione S-transferase Mu 1
hetero molecules

B: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4414
Polymers51,4942
Non-polymers9472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4390 Å2
ΔGint-28 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.830, 51.940, 93.840
Angle α, β, γ (deg.)90.00, 121.08, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer. The asymmetric unit contains three monomers, monomers A and C represent the homodimer, the second dimer can be generated from the monomer B by the operations : -x, y -z.

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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.: 3
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-GDN / GLUTATHIONE S-(2,4 DINITROBENZENE)


Mass: 473.415 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H19N5O10S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.35 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 280 K / Method: vapor diffusion / pH: 6
Details: 20% PEG4000, pH 6.00, 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 24, 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: 2.3→20 Å / Num. all: 32953 / Num. obs: 27431 / % possible obs: 83.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.4 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.051 / Net I/σ(I): 10.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1528 / Rsym value: 0.302 / % possible all: 47.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CCP4model building
CNS1refinement
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GTU

1gtu


Resolution: 2.3→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 100000 / 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
Rfree0.281 822 3 %RANDOM
Rwork0.243 ---
all0.256 27431 --
obs0.243 26990 82.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.6304 Å2 / ksol: 0.27122 e/Å3
Displacement parametersBiso mean: 55.6 Å2
Baniso -1Baniso -2Baniso -3
1--10.75 Å20 Å2-5.06 Å2
2--20.04 Å20 Å2
3----9.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 96 159 5667
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_mcbond_it2.722.5
X-RAY DIFFRACTIONc_mcangle_it4.894
X-RAY DIFFRACTIONc_scbond_it4.114
X-RAY DIFFRACTIONc_scangle_it76
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.439 82 2.8 %
Rwork0.436 2848 -
obs-2848 54.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3GSDNB.PARAMGSDNB.TOP

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