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- PDB-2gsq: GLUTATHIONE S-TRANSFERASE FROM SQUID DIGESTIVE GLAND COMPLEXED WI... -

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Basic information

Entry
Database: PDB / ID: 2gsq
TitleGLUTATHIONE S-TRANSFERASE FROM SQUID DIGESTIVE GLAND COMPLEXED WITH S-(3-IODOBENZYL)GLUTATHIONE
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / SQUID DIGESTIVE GLAND / SIGMA CLASS
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm
Similarity search - Function
S-crystallin / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...S-crystallin / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / 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
S-(3-IODOBENZYL)GLUTATHIONE / Glutathione S-transferase
Similarity search - Component
Biological speciesOmmastrephes sloani (Sloane's squid)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsJi, X. / Armstrong, R.N. / Gilliland, G.L.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Location of a potential transport binding site in a sigma class glutathione transferase by x-ray crystallography.
Authors: Ji, X. / von Rosenvinge, E.C. / Johnson, W.W. / Armstrong, R.N. / Gilliland, G.L.
#1: Journal: Biochemistry / Year: 1995
Title: Three-Dimensional Structure, Catalytic Properties and Evolution of a Sigma Class Glutathione Transferase from Squid, a Progenitor of the Lens-Crystallins of Cephalopods
Authors: Ji, X. / Von Rosenvinge, E.C. / Johnson, W.W. / Tomarev, S.I. / Piatigorsky, J. / Armstrong, R.N. / Gilliland, G.L.
History
DepositionApr 14, 1995Processing site: BNL
Revision 1.0Apr 12, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_database_status / pdbx_struct_special_symmetry / 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 / _pdbx_database_status.process_site / _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)23,9634
Polymers22,8211
Non-polymers1,1433
Water3,801211
1
A: GLUTATHIONE S-TRANSFERASE
hetero molecules

A: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9278
Polymers45,6412
Non-polymers2,2856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7290 Å2
ΔGint-63 kcal/mol
Surface area16940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)73.150, 73.150, 94.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: CIS PROLINE - PRO 51
Components on special symmetry positions
IDModelComponents
11A-204-

GBI

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE / SQUID GST


Mass: 22820.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ommastrephes sloani (Sloane's squid) / Gene: CDNA INSERT OF CLONE PGST5 / Organ: DIGESTIVE GLAND / Plasmid: GST5/PET / Gene (production host): CDNA INSERT OF CLONE PGST5 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A / References: UniProt: P46088, glutathione transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GBI / S-(3-IODOBENZYL)GLUTATHIONE


Mass: 523.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H22IN3O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 3.21 Å3/Da / Density % sol: 61.68 %
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16-8 mg/mlprotein1drop
225 mMTris-HCl1drop
31 mMEDTA1drop
42 mMGSBzI1drop
540 %satammonium sulfate1drop
660-70 %satammonium sulfate1reservoir

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Data collection

DetectorType: ELECTRONICS COMPUTING TECHNOLOGIES / Detector: AREA DETECTOR / Date: May 29, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 15331 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.09
Reflection
*PLUS
Highest resolution: 2.2 Å / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.34 Å / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
PROLSQrefinement
XENGENdata reduction
RefinementResolution: 2.2→6 Å / σ(F): 2 /
RfactorNum. reflection
obs0.173 11649
Displacement parametersBiso mean: 23.12 Å2
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 61 211 1870
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0370.036
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.7081
X-RAY DIFFRACTIONp_mcangle_it1.1981.5
X-RAY DIFFRACTIONp_scbond_it1.2941.5
X-RAY DIFFRACTIONp_scangle_it1.9642
X-RAY DIFFRACTIONp_plane_restr0.0230.03
X-RAY DIFFRACTIONp_chiral_restr0.2140.2
X-RAY DIFFRACTIONp_singtor_nbd0.1980.3
X-RAY DIFFRACTIONp_multtor_nbd0.210.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.190.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor45
X-RAY DIFFRACTIONp_staggered_tor22.815
X-RAY DIFFRACTIONp_orthonormal_tor29.915
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
σ(I): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS

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