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- PDB-3q74: Crystal Structure Analysis of the L7A Mutant of the Apo Form of H... -

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Basic information

Entry
Database: PDB / ID: 3q74
TitleCrystal Structure Analysis of the L7A Mutant of the Apo Form of Human Alpha Class Glutathione Transferase
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: 1.79 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 the L7A Mutant of the Apo Form of Human Alpha Class Glutathione Transferase
Authors: Khoza, T.N. / Fanucchi, S. / Achilonu, I.A. / Fernandes, M.A. / Dirr, H.W.
History
DepositionJan 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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)50,9942
Polymers50,9942
Non-polymers00
Water9,170509
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-23 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.345, 91.317, 51.374
Angle α, β, γ (deg.)90.000, 93.010, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-240-

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: 25496.846 Da / Num. of mol.: 2 / Mutation: L7A
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.: 509 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 293 K / Method: hanging drop / pH: 7.5
Details: 0.1 M Tris, 20% PEG 3350, 2 mM DTT, 0.02% azide, pH 7.5, 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: 8.44 % / Av σ(I) over netI: 84.88 / Number: 360627 / Rsym value: 0.407 / D res high: 1.798 Å / Num. obs: 42718 / % possible obs: 99.48
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRsym value
1.81.8610.736
1.861.9410.667
1.942.0310.57
2.032.1310.507
2.132.2710.467
2.272.4410.454
2.442.6910.428
2.693.0710.411
3.073.8710.4
ReflectionResolution: 1.79→51.3 Å / Num. obs: 42718 / % possible obs: 99.48 % / Redundancy: 8.44 % / Biso Wilson estimate: 15.997 Å2 / Rsym value: 0.407 / Net I/σ(I): 84.88
Reflection shell
Resolution (Å)Rsym value
1.79-1.8620.736
1.862-1.9370.667
1.937-2.0250.57
2.025-2.1320.507
2.132-2.2650.467
2.265-2.440.454
2.44-2.6860.428
2.686-3.0740.411
3.074-3.8730.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.77 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å51.3 Å
Translation2.5 Å51.3 Å

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Processing

Software
NameVersionClassificationNB
SAINTV7.34Adata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→51.3 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.885 / WRfactor Rfree: 0.2546 / WRfactor Rwork: 0.1912 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7982 / SU B: 8.579 / SU ML: 0.115 / SU R Cruickshank DPI: 0.1453 / SU Rfree: 0.1527 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2705 2152 5.1 %RANDOM
Rwork0.2026 ---
obs0.2059 42602 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 64.8 Å2 / Biso mean: 18.019 Å2 / Biso min: 7.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.12 Å2
2--0.04 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.79→51.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 0 509 3861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223408
X-RAY DIFFRACTIONr_angle_refined_deg1.9022.0054590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37724.207145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08315659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.941520
X-RAY DIFFRACTIONr_chiral_restr0.1340.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212504
X-RAY DIFFRACTIONr_mcbond_it1.0111.52081
X-RAY DIFFRACTIONr_mcangle_it1.71623354
X-RAY DIFFRACTIONr_scbond_it3.01431327
X-RAY DIFFRACTIONr_scangle_it4.6734.51236
LS refinement shellResolution: 1.79→1.841 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 155 -
Rwork0.365 2824 -
all-2979 -
obs--93.27 %
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)
10.5754-0.0952-0.45190.3212-0.05560.6467-0.06170.0335-0.03810.07260.01450.06150.0408-0.03990.04720.0826-0.00040.03360.05820.00370.106312.278-16.53716.374
20.5981-0.2093-0.40120.86220.25360.4295-0.005-0.01750.0550.04360.0539-0.11030.02870.0151-0.04880.07050.00040.0110.0604-0.00940.108134.77-15.8645.811
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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