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- PDB-3vln: Human Glutathione Transferase O1-1 C32S Mutant in Complex with As... -

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Basic information

Entry
Database: PDB / ID: 3vln
TitleHuman Glutathione Transferase O1-1 C32S Mutant in Complex with Ascorbic Acid
ComponentsGlutathione S-transferase omega-1
KeywordsTRANSFERASE / GST fold / reductase / glutathione
Function / homology
Function and homology information


positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / methylarsonate reductase / methylarsonate reductase activity / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / Methylation / cellular response to arsenic-containing substance / Glutathione conjugation ...positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / methylarsonate reductase / methylarsonate reductase activity / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / Methylation / cellular response to arsenic-containing substance / Glutathione conjugation / positive regulation of ryanodine-sensitive calcium-release channel activity / glutathione transferase / glutathione transferase activity / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / glutathione metabolic process / xenobiotic catabolic process / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / oxidoreductase activity / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, omega-class / Glutathione S-transferase Omega/Tau-like / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / 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 ...Glutathione S-transferase, omega-class / Glutathione S-transferase Omega/Tau-like / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / 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
ACETATE ION / ASCORBIC ACID / Glutathione S-transferase omega-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBrock, J. / 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 2, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / struct_ref_seq_dif ...chem_comp / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_ref_seq_dif.details / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3539
Polymers27,5841
Non-polymers7708
Water3,693205
1
A: Glutathione S-transferase omega-1
hetero molecules

A: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,70718
Polymers55,1682
Non-polymers1,53916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area6030 Å2
ΔGint-108 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.918, 56.918, 140.511
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 27583.779 Da / Num. of mol.: 1 / Mutation: C32S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTO1, GSTTLP28 / Plasmid: pHUE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P78417, glutathione transferase
#3: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Comment: medication*YM

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Non-polymers , 5 types, 212 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.75
Details: 2.2M ammonium sulfate, 0.1M sodium acetate pH 4.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2009 / Details: BEAMLINE OPTICS
RadiationMonochromator: BEAMLINE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→49.29 Å / Num. all: 29768 / Num. obs: 29768 / % possible obs: 99.2 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 40.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 4.14 / Num. unique all: 2912 / % possible all: 98.7

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Processing

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

1eem


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.773 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21749 1507 5.1 %RANDOM
Rwork0.18043 ---
obs0.18222 28239 99.24 %-
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: 31.695 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20.42 Å2-0 Å2
2--0.84 Å2-0 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 47 205 2175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222065
X-RAY DIFFRACTIONr_bond_other_d0.0010.021465
X-RAY DIFFRACTIONr_angle_refined_deg1.862.0052797
X-RAY DIFFRACTIONr_angle_other_deg1.0233592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09524.83591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15315378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.39159
X-RAY DIFFRACTIONr_chiral_restr0.1110.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212247
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02397
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9931.51226
X-RAY DIFFRACTIONr_mcbond_other0.3061.5485
X-RAY DIFFRACTIONr_mcangle_it1.70121988
X-RAY DIFFRACTIONr_scbond_it2.6733839
X-RAY DIFFRACTIONr_scangle_it4.1494.5802
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 107 -
Rwork0.234 2020 -
obs--97.61 %
Refinement TLS params.Method: refined / Origin x: 22.7624 Å / Origin y: -10.6049 Å / Origin z: 19.8133 Å
111213212223313233
T0.0374 Å20.0008 Å20.0009 Å2-0.0298 Å2-0.0051 Å2--0.0971 Å2
L1.0462 °20.225 °20.1619 °2-1.7715 °2-0.1176 °2--3.6391 °2
S0.0029 Å °-0.0807 Å °0.1159 Å °0.09 Å °-0.0344 Å °0.057 Å °-0.3497 Å °-0.0532 Å °0.0314 Å °

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