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- PDB-1yj6: crystal structure of human glutathione S-transferase M1A-1A compl... -

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Basic information

Entry
Database: PDB / ID: 1yj6
Titlecrystal structure of human glutathione S-transferase M1A-1A complexed with glutathionyl-zinc-trihydroxide
ComponentsGlutathione S-transferase Mu 1
KeywordsTRANSFERASE / glutathione / conjugation / detoxification / cytosolic / dimer / active site / zinc / coordination complex
Function / homology
Function and homology information


nitrobenzene metabolic process / cellular detoxification of nitrogen compound / glutathione binding / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / Glutathione conjugation / Paracetamol ADME / Azathioprine ADME / prostaglandin metabolic process / intercellular bridge ...nitrobenzene metabolic process / cellular detoxification of nitrogen compound / glutathione binding / hepoxilin biosynthetic process / 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: 2.5 Å
AuthorsPatskovsky, Y.V. / Patskovska, L.N. / Listowsky, I. / Almo, S.C.
Citation
Journal: To be Published
Title: Human Glutathione S-Transferase M1A-1A Catalyzes Formation of Gsh-Metal Complexes
Authors: Patskovsky, Y.V. / Patskovska, L.N. / Listowsky, I. / Almo, S.C.
#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
DepositionJan 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)78,3599
Polymers77,2413
Non-polymers1,1186
Water1,910106
1
A: Glutathione S-transferase Mu 1
B: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2396
Polymers51,4942
Non-polymers7454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-96 kcal/mol
Surface area18670 Å2
MethodPISA
2
C: Glutathione S-transferase Mu 1
hetero molecules

C: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2396
Polymers51,4942
Non-polymers7454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Unit cell
Length a, b, c (Å)178.640, 51.410, 93.820
Angle α, β, γ (deg.)90.00, 122.47, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a homodimer. The asymmetric unit contains one full homodimer (chains A,B) and a monomer (chain C)

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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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


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


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.38 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 280 K / Method: vapor diffusion / pH: 6
Details: PEG4000, GSH, Zinc chloride, 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: Nov 20, 2004 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 23285 / Num. obs: 23285 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.049 / Net I/σ(I): 7.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1544 / Rsym value: 0.39 / % possible all: 61.2

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Processing

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

1gtu


Resolution: 2.5→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 137983.26 / 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
Rfree0.264 674 3 %RANDOM
Rwork0.23 ---
all0.24 23285 --
obs0.23 22694 89.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.272049 e/Å3
Displacement parametersBiso mean: 49.7 Å2
Baniso -1Baniso -2Baniso -3
1--9.04 Å20 Å22.28 Å2
2--13.28 Å20 Å2
3----4.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.77 Å0.73 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 72 97 5581
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_mcbond_it2.432
X-RAY DIFFRACTIONc_mcangle_it3.723.5
X-RAY DIFFRACTIONc_scbond_it3.943.5
X-RAY DIFFRACTIONc_scangle_it5.514.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 89 3.1 %
Rwork0.401 2779 -
obs-2779 68.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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