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- PDB-1vf2: cGSTA1-1 in complex with S-hexyl-glutathione -

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Basic information

Entry
Database: PDB / ID: 1vf2
TitlecGSTA1-1 in complex with S-hexyl-glutathione
ComponentsGlutathione S-transferase 3
KeywordsTRANSFERASE / glutathione / detoxification
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / xenobiotic metabolic process / glutathione metabolic process / cytoplasm
Similarity search - Function
Glutathione S-transferase, alpha class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / 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 / 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, alpha class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / 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 / 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
S-HEXYLGLUTATHIONE / Glutathione S-transferase 3
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLin, S.C. / Lo, Y.C. / Tam, M.F. / Liaw, Y.C.
CitationJournal: To be Published
Title: Crystal structures of chicken glutathione S-transferase A1-1
Authors: Lin, S.C. / Lo, Y.C. / Tam, M.F. / Liaw, Y.C.
History
DepositionApr 7, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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 3
B: Glutathione S-transferase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5765
Polymers52,7262
Non-polymers8503
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-52 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.316, 115.346, 95.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Glutathione S-transferase 3 / glutathione S-transferase A1-1 / GST-CL3 / GST class-alpha


Mass: 26362.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: GTA3 / Plasmid: pBAce / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P26697, glutathione transferase
#2: Chemical ChemComp-GTX / S-HEXYLGLUTATHIONE


Mass: 392.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30N3O6S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.64 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: sodium cacodylate, magnesium acetate, zinc acetate, PEG8000, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 17, 1998 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→29.28 Å / Num. all: 30228 / Num. obs: 30228 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Redundancy: 7.46 % / Biso Wilson estimate: 25.8 Å2 / Limit h max: 46 / Limit h min: 0 / Limit k max: 53 / Limit k min: 0 / Limit l max: 43 / Limit l min: 0 / Observed criterion F max: 539448.37 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.2
Reflection shellResolution: 2.15→2.25 Å / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.23 / % possible all: 89.1

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Processing

Software
NameVersionClassificationNB
CNS1refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GUH

1guh


Resolution: 2.15→29.28 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2890 10 %random
Rwork0.204 ---
all-30647 --
obs-28768 93.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 57.3469 Å2 / ksol: 0.350262 e/Å3
Displacement parametersBiso max: 87.33 Å2 / Biso mean: 45.03 Å2 / Biso min: 20.53 Å2
Baniso -1Baniso -2Baniso -3
1-19.28 Å20 Å20 Å2
2---18.02 Å20 Å2
3----1.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.33 Å
Luzzati d res high-2.15
Refinement stepCycle: LAST / Resolution: 2.15→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3652 0 53 102 3807
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.15-2.250.3462927.70.31826270.0193788291977.1
2.25-2.370.2923328.80.26630060.0153774333888.4
2.37-2.510.2933649.60.24532090.0133798357394.1
2.51-2.710.26538810.20.22832590.0123803364795.9
2.71-2.980.27734590.22133660.0123822371197.1
2.98-3.410.256384100.21633850.0113828376998.5
3.41-4.30.2033829.90.16934630.0093863384599.5
4.3-29.280.20640310.10.18235630.0093995396699.2
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 DIFFRACTION4gtx.paramgtx.top

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