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- PDB-2f3m: Structure of human GLUTATHIONE S-TRANSFERASE M1A-1A complexed wit... -

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Basic information

Entry
Database: PDB / ID: 2f3m
TitleStructure of human GLUTATHIONE S-TRANSFERASE M1A-1A complexed with 1-(S-(GLUTATHIONYL)-2,4,6-TRINITROCYCLOHEXADIENATE ANION
ComponentsGlutathione S-transferase Mu 1
KeywordsTRANSFERASE / GLUTATHIONE / CONJUGATION / DETOXIFICATION / CYTOSOLIC / DIMER / ACTIVE SITE / TRANSITION STATE ANALOGUE
Function / homology
Function and homology information


nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / glutathione binding / Glutathione conjugation / Paracetamol ADME / Azathioprine ADME / prostaglandin metabolic process / glutathione transferase ...nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / glutathione binding / Glutathione conjugation / Paracetamol ADME / Azathioprine ADME / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / xenobiotic catabolic process / intercellular bridge / 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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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
Chem-GTD / Glutathione S-transferase Mu 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionNov 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: Glutathione S-transferase Mu 1
E: Glutathione S-transferase Mu 1
F: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,60412
Polymers154,4816
Non-polymers3,1236
Water95553
1
A: Glutathione S-transferase Mu 1
B: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5354
Polymers51,4942
Non-polymers1,0412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-36 kcal/mol
Surface area18900 Å2
MethodPISA
2
C: Glutathione S-transferase Mu 1
D: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5354
Polymers51,4942
Non-polymers1,0412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-35 kcal/mol
Surface area18820 Å2
MethodPISA
3
E: Glutathione S-transferase Mu 1
F: Glutathione S-transferase Mu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5354
Polymers51,4942
Non-polymers1,0412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-35 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.965, 93.096, 92.998
Angle α, β, γ (deg.)120.53, 106.19, 89.97
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 1 - 217 / Label seq-ID: 2 - 218

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
DetailsThe biological assembly is a homodimer composed of two identical monomers. The unit cell/asymmetric unit contains 3 full 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.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTM1, GST1 / Plasmid: pET3a / 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-GTD / 1-(S-GLUTATHIONYL)-2,4,6-TRINITROCYCLOHEXA-2,5-DIENE / (S)-2-AMINO-5-((R)-1-(CARBOXYMETHYLAMINO)-1-OXO-3-(2,4,6-TRINITROCYCLOHEXA-2,5-DIENYLTHIO)PROPAN-2-YLAMINO)-5-OXOPENTANOIC ACID


Mass: 520.428 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H20N6O12S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 47.15 %
Crystal growTemperature: 280 K / pH: 6
Details: 20% PEG 4000, 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
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 11, 2005 / 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: 2.667→100 Å / Num. obs: 38744 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.068 / Rsym value: 0.042 / Net I/σ(I): 7.8
Reflection shellResolution: 2.67→2.8 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.32 / % possible all: 95.1

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Processing

Software
NameVersionClassification
HKL-2000data reduction
CCP4model building
REFMAC5.2.0005refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GTU

1gtu


Resolution: 2.7→20 Å / SU B: 20.024 / SU ML: 0.381 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1169 3.1 %RANDOM
Rwork0.233 ---
obs0.234 36687 97.1 %-
all-36687 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.38 Å2
Baniso -1Baniso -2Baniso -3
1-5.56 Å2-0.1 Å2-0.99 Å2
2---3.49 Å2-2.52 Å2
3----5.19 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10904 0 210 53 11167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211430
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.171.99615433
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.07751318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.32124.011541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.748152086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4841560
X-RAY DIFFRACTIONr_chiral_restr0.0820.21592
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028718
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2550.35198
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3370.57932
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.5763
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.410.3106
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5750.517
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.73926704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.272310620
X-RAY DIFFRACTIONr_scbond_it0.4635339
X-RAY DIFFRACTIONr_scangle_it0.25214805
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1789 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight positional0.040.05
3Ctight positional0.040.05
4Dtight positional0.040.05
5Etight positional0.040.05
6Ftight positional0.040.05
1Atight thermal0.070.5
2Btight thermal0.070.5
3Ctight thermal0.070.5
4Dtight thermal0.070.5
5Etight thermal0.070.5
6Ftight thermal0.070.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 84 -
Rwork0.386 2656 -
obs--95.37 %

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