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- PDB-1ydk: Crystal structure of the I219A mutant of human glutathione transf... -

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Basic information

Entry
Database: PDB / ID: 1ydk
TitleCrystal structure of the I219A mutant of human glutathione transferase A1-1 with S-hexylglutathione
ComponentsGlutathione S-transferase A1
KeywordsTRANSFERASE / Glutathione transferase / S-hexylglutathione
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / steroid delta-isomerase activity / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process ...Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / steroid delta-isomerase activity / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / glutathione metabolic process / epithelial cell differentiation / xenobiotic metabolic process / fatty acid binding / extracellular exosome / cytosol
Similarity search - Function
Glutathione S-transferase, alpha class / 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, alpha class / 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
S-HEXYLGLUTATHIONE / Glutathione S-transferase A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKuhnert, D.C. / Sayed, Y. / Mosebi, S. / Sayed, M. / Sewell, T. / Dirr, H.W.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Tertiary Interactions Stabilise the C-terminal Region of Human Glutathione Transferase A1-1: a Crystallographic and Calorimetric Study.
Authors: Kuhnert, D.C. / Sayed, Y. / Mosebi, S. / Sayed, M. / Sewell, T. / Dirr, H.W.
History
DepositionDec 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase A1
B: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0414
Polymers51,2562
Non-polymers7852
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-34 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.530, 91.472, 51.482
Angle α, β, γ (deg.)90.00, 92.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-6191-

HOH

21A-6207-

HOH

31B-6237-

HOH

41B-6317-

HOH

DetailsThe asymmetric unit is a dimer which is the known biological unit

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Components

#1: Protein Glutathione S-transferase A1 / / GTH1 / HA subunit 1 / GST- epsilon / GSTA1-1 / GST class-alpha


Mass: 25628.041 Da / Num. of mol.: 2 / Mutation: I219A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTA1 / Plasmid: pKHA1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P08263, glutathione transferase
#2: Chemical ChemComp-GTX / S-HEXYLGLUTATHIONE


Mass: 392.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.39 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 2000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 29853 / Num. obs: 29853 / % possible obs: 92.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.055 / Χ2: 0.9
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2 % / Rmerge(I) obs: 0.275 / Num. unique all: 2163 / Χ2: 2.219 / % possible all: 67.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement
PDB_EXTRACT1.501data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K3L

1k3l


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.416 / SU ML: 0.128 / SU R Cruickshank DPI: 0.225 / Cross valid method: THROUGHOUT / ESU R Free: 0.191 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1515 5 %RANDOM
Rwork0.203 ---
all0.205 29016 --
obs0.218 29853 90.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.528 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20.52 Å2
2--1.01 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3453 0 52 409 3914
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.00835730.022
X-RAY DIFFRACTIONr_angle_refined_deg1.01247992.005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0174245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0215224.079
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39569515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4772215
X-RAY DIFFRACTIONr_chiral_restr0.0725210.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00326160.02
X-RAY DIFFRACTIONr_nbd_refined0.18419080.2
X-RAY DIFFRACTIONr_nbtor_refined0.30224340.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1113650.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.121300.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.117160.2
X-RAY DIFFRACTIONr_mcbond_it0.4222411.5
X-RAY DIFFRACTIONr_mcangle_it0.68334422
X-RAY DIFFRACTIONr_scbond_it0.97215393
X-RAY DIFFRACTIONr_scangle_it1.49513574.5
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 64 -
Rwork0.33 1251 -
obs--53.37 %

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