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- PDB-1gne: THE THREE-DIMENSIONAL STRUCTURE OF GLUTATHIONE S-TRANSFERASE OF S... -

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Basic information

Entry
Database: PDB / ID: 1gne
TitleTHE THREE-DIMENSIONAL STRUCTURE OF GLUTATHIONE S-TRANSFERASE OF SCHISTOSOMA JAPONICUM FUSED WITH A CONSERVED NEUTRALIZING EPITOPE ON GP41 OF HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / GLUTATHIONE TRANSFERASE
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function
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, 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 class-mu 26 kDa isozyme
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsLim, K. / Ho, J.X. / Keeling, K. / Gilliland, G.L. / Ji, X. / Ruker, F. / Carter, D.C.
Citation
Journal: Protein Sci. / Year: 1994
Title: Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV.
Authors: Lim, K. / Ho, J.X. / Keeling, K. / Gilliland, G.L. / Ji, X. / Ruker, F. / Carter, D.C.
#1: Journal: PROTEIN PEPT.LETT. / Year: 1994
Title: Fusion Proteins as Alternate Crystallization Paths to Difficult Structure Problems
Authors: Carter, D.C. / Ruker, F. / Ho, J.X. / Lim, K. / Keeling, K. / Gilliland, G.L. / Ji, X.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Molecular Structure at 1.8 Angstroms of Mouse Liver Class Pi Glutathione S-Transferase Complexed with S-(P-Nitrobenzyl)Glutathione and Other Inhibitors
Authors: Garcia-Saez, I. / Parraga, A. / Phillips, M.F. / Mantle, T.J. / Coll, M.
#3: Journal: Curr.Opin.Struct.Biol. / Year: 1993
Title: Glutathione Proteins
Authors: Gilliland, G.L.
#4: Journal: J.Virol. / Year: 1993
Title: A Conserved Neutralizing Epitope on Gp41 of Human Immunodeficiency Virus Type 1
Authors: Muster, T. / Steindl, F. / Purtscher, M. / Trkola, A. / Klima, A. / Himmler, G. / Ruker, F. / Katinger, H.
#5: Journal: J.Mol.Biol. / Year: 1993
Title: Structure Determination and Refinement of Human Alpha Class Glutathione Transferase A1-1, and a Comparison with the Mu and Pi Class Enzymes
Authors: Sinning, I. / Kleywegt, G.J. / Cowan, S.W. / Reinemer, P. / Dirr, H.W. / Huber, R. / Gilliland, G.L. / Armstrong, R.N. / Ji, X. / Board, P.G. / Olin, B. / Mannervik, B. / Jones, T.A.
#6: Journal: Biochemistry / Year: 1992
Title: The Three-Dimensional Structure of a Glutathione S-Transferase from the Mu Gene Class. Structural Analysis of the Binary Complex of Isoenzyme 3-3 and Glutathione at 2.2 Angstroms Resolution
Authors: Ji, X. / Zhang, P. / Armstrong, R.N. / Gilliland, G.L.
#7: Journal: J.Mol.Biol. / Year: 1992
Title: Three-Dimensional Structure of Class P Glutathione S-Transferase from Human Placenta in Complex with S-Hexylglutathione at 2.8 Angstroms Resolution
Authors: Reinemer, P. / Dirr, H.W. / Ladenstein, R. / Huber, R. / Lobello, M. / Federici, G. / Parker, M.W.
#8: Journal: Embo J. / Year: 1991
Title: The Three-Dimensional Structure of Class P Glutathione S-Transferase in Complex with Glutathione Sulfonate at 2.3 Angstroms Resolution
Authors: Reinemer, P. / Dirr, H.W. / Ladenstein, R. / Schiffer, J. / Gallay, O. / Huber, R.
#9: Journal: Gene / Year: 1988
Title: Single-Step Purification of Polypeptides Expressed in Escherichia Coli as Fusions with Glutathione S-Transferase
Authors: Smith, D.B. / Johnson, K.S.
#10: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Correction
Authors: Smith, D.B. / Davern, K.M. / Board, P.G. / Tiu, W.U. / Garcia, E.G. / Mitchell, G.F.
#11: Journal: Proc.Natl.Acad.Sci.USA / Year: 1986
Title: Mr 26,000 Antigen of Schistosoma Japonicum Recognized by Resistant Wehi 129(Slash)J Mice is a Parasite Glutathione S-Transferase
Authors: Smith, D.B. / Davern, K.M. / Board, P.G. / Tiu, W.U. / Garcia, E.G. / Mitchell, G.F.
History
DepositionJun 16, 1994Processing site: BNL
Revision 1.0Nov 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 21, 2012Group: Non-polymer description
Revision 1.4Feb 20, 2013Group: Database references
Revision 1.5Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.6Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.7Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.8Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3992
Polymers27,0911
Non-polymers3071
Water2,270126
1
A: GLUTATHIONE S-TRANSFERASE
hetero molecules

A: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7984
Polymers54,1832
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)94.740, 94.740, 58.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: CIS PROLINE - PRO 55 / 2: CIS PROLINE - PRO 201
3: HIS 214 - PRO 215 OMEGA = 246.61 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE


Mass: 27091.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: GP41 / Organ: LIVER / Gene (production host): GP41 / References: UniProt: P08515, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
260 %(w/v)PEG33501drop
350 mMpotassium phosphate1drop
460 %(w/v)PEG33501reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 8485 / % possible obs: 86.9 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.117

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Processing

Software
NameClassification
X-PLORmodel building
GPRLSArefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.219 -
obs0.219 7622
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 20 126 2051
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.03
X-RAY DIFFRACTIONx_angle_d1.2
X-RAY DIFFRACTIONx_planar_d0.030.023
X-RAY DIFFRACTIONx_plane_restr0.040.034
X-RAY DIFFRACTIONx_chiral_restr0.20.269
X-RAY DIFFRACTIONx_mcbond_it1.51.3
X-RAY DIFFRACTIONx_scbond_it21.269
X-RAY DIFFRACTIONx_mcangle_it21.95
X-RAY DIFFRACTIONx_scangle_it1.51.6

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