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- PDB-1tdi: Crystal Structure of hGSTA3-3 in Complex with Glutathione -

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Basic information

Entry
Database: PDB / ID: 1tdi
TitleCrystal Structure of hGSTA3-3 in Complex with Glutathione
ComponentsGlutathione S-transferase A3-3
KeywordsTRANSFERASE / GST / hGSTA3-3 / steroid isomerase
Function / homology
Function and homology information


Glutathione conjugation / NFE2L2 regulating anti-oxidant/detoxification enzymes / glutathione transferase / glutathione transferase activity / glutathione metabolic process / xenobiotic metabolic process / lipid metabolic process / extracellular exosome / cytosol
Similarity search - Function
Glutathione S-transferase, alpha class / Glutathione S-transferase, C-terminal domain / : / 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 / Glutathione S-transferase, C-terminal-like ...Glutathione S-transferase, alpha class / Glutathione S-transferase, C-terminal domain / : / 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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-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 / Glutathione S-transferase A3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGu, Y. / Guo, J. / Pal, A. / Pan, S.S. / Zimniak, P. / Singh, S.V. / Ji, X.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal structure of human glutathione S-transferase A3-3 and mechanistic implications for its high steroid isomerase activity.
Authors: Gu, Y. / Guo, J. / Pal, A. / Pan, S.S. / Zimniak, P. / Singh, S.V. / Ji, X.
History
DepositionMay 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 17, 2014Group: Other
Revision 1.4Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase A3-3
B: Glutathione S-transferase A3-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2924
Polymers50,6772
Non-polymers6152
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-28 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.985, 95.588, 114.039
Angle α, β, γ (deg.)90.00, 90.14, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.936454, 0.349223, 0.033125), (0.349213, -0.937022, 0.006258), (0.033225, 0.005707, -0.999432)23.15293, 44.2916, 83.06289
3generate(-0.999763, -0.020701, -0.006767), (0.020588, -0.999654, 0.016347), (-0.007103, 0.016204, 0.999843)22.23379, 0.69264, 57.117
4generate(-0.99997, 0.006554, -0.004142), (-0.00652, -0.999945, -0.008262), (-0.004196, -0.008234, 0.999957)46.32733, 49.36661, 50.5662

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Components

#1: Protein Glutathione S-transferase A3-3 / GST class-alpha / hGSTA3-3


Mass: 25338.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTA3 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q16772, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.71 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 288 K / Method: vapor diffusion / pH: 8
Details: PEG 6000, Na-HEPES, pH 8.0, VAPOR DIFFUSION, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: Dec 12, 1999 / Details: mirrors
RadiationMonochromator: OSMIC MIRRORS SYSTEM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 78184 / Num. obs: 74040 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.38 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 9.12
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.28 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.94 / Num. unique all: 7051 / % possible all: 9.9

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GUH

1guh


Resolution: 2.4→29.75 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1738491.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2963 5.1 %RANDOM
Rwork0.228 ---
all0.252 78184 --
obs0.228 58496 74.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.4335 Å2 / ksol: 0.331681 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1--9.12 Å20 Å2-0.22 Å2
2--14.7 Å20 Å2
3----5.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.32 Å
Luzzati d res low-30 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3502 0 40 274 3816
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it2.971.5
X-RAY DIFFRACTIONc_mcangle_it4.142
X-RAY DIFFRACTIONc_scbond_it5.12
X-RAY DIFFRACTIONc_scangle_it6.732.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.289 221 5.6 %
Rwork0.259 3710 -
obs--50.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4PARAM.GSHTOPOL.GSH

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