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- PDB-3u6v: Crystal Structure Analysis of L23A mutant of human GST A1-1 -

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Basic information

Entry
Database: PDB / ID: 3u6v
TitleCrystal Structure Analysis of L23A mutant of human GST A1-1
ComponentsGlutathione S-transferase A1
KeywordsTRANSFERASE / Glutathione Transferase / thioredoxin / conserved residues / hydrophobic core
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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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-transferase A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsFanucchi, S. / Achilonu, I.A. / Khoza, T.N. / Fernandes, M.A. / Gildenhuys, S. / Dirr, H.W.
CitationJournal: To be Published
Title: Crystal Structure Analysis of L23A mutant of human GST A1-1
Authors: Khoza, T.N. / Fanucchi, S. / Achilonu, I.A. / Fernandes, M.A. / Dirr, H.W.
History
DepositionOct 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,2562
Polymers51,2562
Non-polymers00
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-22 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.195, 94.125, 51.571
Angle α, β, γ (deg.)90.000, 92.530, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-306-

HOH

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Components

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


Mass: 25628.041 Da / Num. of mol.: 2 / Mutation: L23A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTA1 / Plasmid: pKHA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08263, glutathione transferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris, 20% PEG 3350, 2 mM DTT, 0.02% azide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Oct 5, 2009 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 7.51 % / Av σ(I) over netI: 140.51 / Number: 183184 / Rsym value: 0.317 / D res high: 2.194 Å / Num. obs: 24385 / % possible obs: 99.59
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRsym value
2.192.2710.916
2.272.3611.018
2.362.4710.955
2.472.610.895
2.62.7610.804
2.762.9810.628
2.983.2810.384
3.283.7510.271
3.754.7310.19
ReflectionResolution: 2.194→68.57 Å / Num. obs: 24385 / % possible obs: 99.59 % / Redundancy: 7.51 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 0.317 / Net I/σ(I): 140.514
Reflection shell
Resolution (Å)Highest resolution (Å)Rsym valueDiffraction-ID
2.194-2.2720.9161
2.272-2.3631.0181
2.363-2.4710.9551
2.471-2.6010.8951
2.601-2.7640.8041
2.764-2.9770.6281
2.977-3.2770.3841
3.277-3.7510.2711
3.751-4.7260.191
4.7260.1421

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 37.93 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å51.52 Å
Translation2.5 Å51.52 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 24378
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.12-10032.60.68512
6.41-8.1236.90.786503
5.59-6.41330.811511
5.06-5.5929.60.844525
4.66-5.0628.30.836560
4.34-4.6625.80.846621
4.07-4.3426.30.831659
3.85-4.0728.50.806697
3.67-3.8526.40.804726
3.5-3.6729.50.785771
3.36-3.531.30.768792
3.23-3.36330.764820
3.12-3.2334.30.754876
3.02-3.1237.40.726896
2.93-3.0235.80.734917
2.84-2.9336.80.742951
2.76-2.8439.40.738976
2.69-2.7638.70.7371025
2.63-2.6938.30.7151010
2.56-2.6338.70.7331036
2.51-2.5638.60.7111100
2.45-2.5138.20.71083
2.4-2.4540.30.691166
2.35-2.442.20.6481108
2.31-2.3544.60.6251197
2.27-2.3143.70.6521196
2.2-2.2752.10.562144

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Processing

Software
NameVersionClassificationNB
SAINTV7.34Adata scaling
SAINTV7.34Adata reduction
PHASER2.1.4phasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→51.52 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.866 / WRfactor Rfree: 0.2715 / WRfactor Rwork: 0.2048 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7736 / SU B: 18.578 / SU ML: 0.209 / SU R Cruickshank DPI: 0.3109 / SU Rfree: 0.2542 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2884 1245 5.1 %RANDOM
Rwork0.2173 ---
obs0.221 24378 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 103.54 Å2 / Biso mean: 30.1988 Å2 / Biso min: 6.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.02 Å2
2---0.3 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.2→51.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3339 0 0 249 3588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223408
X-RAY DIFFRACTIONr_angle_refined_deg1.7042.0064587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9595412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76824.207145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.01615668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5011520
X-RAY DIFFRACTIONr_chiral_restr0.1120.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212496
X-RAY DIFFRACTIONr_mcbond_it0.7951.52072
X-RAY DIFFRACTIONr_mcangle_it1.37923344
X-RAY DIFFRACTIONr_scbond_it2.47131336
X-RAY DIFFRACTIONr_scangle_it3.6824.51243
LS refinement shellResolution: 2.2→2.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 78 -
Rwork0.284 1625 -
all-1703 -
obs--93.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.43920.2186-0.3112.6555-0.83931.6336-0.05280.1440.0579-0.10580.18930.2310.0748-0.4196-0.13640.0418-0.0044-0.03440.13620.02160.0384-33.911919.8889-4.6862
21.72340.0863-0.41961.67590.26922.348-0.06250.1688-0.0511-0.15980.0069-0.17230.10980.00970.05550.03010.00170.0090.0213-0.01240.053-12.119421.5004-15.5929
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 208
2X-RAY DIFFRACTION2B4 - 210

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