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- PDB-3q18: Human Glutathione Transferase O2 -

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Basic information

Entry
Database: PDB / ID: 3q18
TitleHuman Glutathione Transferase O2
ComponentsGlutathione S-transferase omega-2
KeywordsTRANSFERASE / Glutathione Transferase / GST / Dehydroascorbate Reductase / Reductase
Function / homology
Function and homology information


methylarsonate reductase / methylarsonate reductase activity / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / cellular response to arsenic-containing substance / Glutathione conjugation / glutathione transferase / glutathione transferase activity ...methylarsonate reductase / methylarsonate reductase activity / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / cellular response to arsenic-containing substance / Glutathione conjugation / glutathione transferase / glutathione transferase activity / glutathione metabolic process / xenobiotic metabolic process / oxidoreductase activity / extracellular exosome / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, omega-class / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / 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, omega-class / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / 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
DI(HYDROXYETHYL)ETHER / Glutathione S-transferase omega-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhou, H. / Board, P.G. / Oakley, A.J.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural insights into the dehydroascorbate reductase activity of human omega-class glutathione transferases.
Authors: Zhou, H. / Brock, J. / Liu, D. / Board, P.G. / Oakley, A.J.
History
DepositionDec 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Nov 1, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase omega-2
B: Glutathione S-transferase omega-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8096
Polymers55,5402
Non-polymers2694
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-13 kcal/mol
Surface area22170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.659, 85.718, 60.359
Angle α, β, γ (deg.)90.00, 95.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutathione S-transferase omega-2 / GSTO-2


Mass: 27769.898 Da / Num. of mol.: 2 / Mutation: C80S, C121S, C136S, C140S, C170S, C214S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTO2 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15/rep4 / References: UniProt: Q9H4Y5, glutathione transferase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M sodium chloride, 0.1M Bicine pH 9.0, 20% (v/v) PEGMME 2000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.956668 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 1, 2010
RadiationMonochromator: Double Si with sagittaly bent second crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956668 Å / Relative weight: 1
ReflectionResolution: 1.7→40.85 Å / Num. all: 48429 / Num. obs: 48429 / % possible obs: 93.4 % / Observed criterion σ(F): -4 / Observed criterion σ(I): -4 / Redundancy: 3.5 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 14.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 3.5 / Num. unique all: 6623 / % possible all: 87.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EEM

1eem


Resolution: 1.7→34.9 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.964 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18563 3025 6.3 %RANDOM
Rwork0.15743 ---
all0.15918 45361 --
obs0.15918 45361 93.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.446 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å2-0.16 Å2
2---0.1 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3860 0 15 344 4219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224185
X-RAY DIFFRACTIONr_bond_other_d0.0010.022950
X-RAY DIFFRACTIONr_angle_refined_deg1.0341.975721
X-RAY DIFFRACTIONr_angle_other_deg0.81837170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.795521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46722.921202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60615724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1141534
X-RAY DIFFRACTIONr_chiral_restr0.0590.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214641
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02910
X-RAY DIFFRACTIONr_mcbond_it0.3861.52452
X-RAY DIFFRACTIONr_mcbond_other0.0781.5957
X-RAY DIFFRACTIONr_mcangle_it0.76524016
X-RAY DIFFRACTIONr_scbond_it1.26131733
X-RAY DIFFRACTIONr_scangle_it2.1364.51682
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 230 -
Rwork0.184 3121 -
obs-3351 86.93 %
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)
10.7957-0.019-0.09231.38020.53451.33980.0276-0.0033-0.02970.0039-0.0025-0.14090.03770.0782-0.02510.0108-0.0037-0.00140.01010.02170.013212.17870.690328.4518
21.1084-0.4098-0.46421.12810.37631.133-0.00110.01370.10080.01470.017-0.0433-0.0901-0.0171-0.01580.0118-0.0014-0.01770.02860.00940.00023.922915.27442.9079
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 239
2X-RAY DIFFRACTION2B7 - 239

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