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- PDB-2gdr: Crystal structure of a bacterial glutathione transferase -

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Basic information

Entry
Database: PDB / ID: 2gdr
TitleCrystal structure of a bacterial glutathione transferase
Componentsglutathione S-transferase
KeywordsTRANSFERASE / protein homodimer / each monomer contains two domains / N-term domain is mixed beta sheets and alpha helices / C-term domain is alpha helical
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
Glutathione S-transferase, N-terminal domain / 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. ...Glutathione S-transferase, N-terminal domain / 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
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTocheva, E.I. / Fortin, P.D. / Eltis, L.D. / Murphy, M.E.P.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structures of Ternary Complexes of BphK, a Bacterial Glutathione S-Transferase That Reductively Dechlorinates Polychlorinated Biphenyl Metabolites.
Authors: Tocheva, E.I. / Fortin, P.D. / Eltis, L.D. / Murphy, M.E.
History
DepositionMar 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 14, 2011Group: Non-polymer description
Revision 1.4Aug 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glutathione S-transferase
B: glutathione S-transferase
C: glutathione S-transferase
D: glutathione S-transferase
E: glutathione S-transferase
F: glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,37515
Polymers133,6096
Non-polymers2,7669
Water3,873215
1
A: glutathione S-transferase
B: glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4585
Polymers44,5362
Non-polymers9223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-27 kcal/mol
Surface area15860 Å2
MethodPISA
2
C: glutathione S-transferase
D: glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4585
Polymers44,5362
Non-polymers9223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-30 kcal/mol
Surface area15820 Å2
MethodPISA
3
E: glutathione S-transferase
F: glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4585
Polymers44,5362
Non-polymers9223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-29 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.440, 103.440, 262.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
glutathione S-transferase


Mass: 22268.111 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: bphK / Production host: Escherichia coli (E. coli)
References: GenBank: 27528348, UniProt: Q59721*PLUS, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal growTemperature: 323 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1M K/Na tartrate, 0.1 M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 323K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97974 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97974 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 92159 / Num. obs: 92159 / % possible obs: 97 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.061
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.384 / % possible all: 95.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GDH

2gdh
PDB Unreleased entry


Resolution: 2.1→50 Å / Isotropic thermal model: Isotropic / Stereochemistry target values: Engh & Huber
Details: The twinning operator is h,-h-k,-l. The twinning fraction is 0.45.
RfactorNum. reflectionSelection details
Rfree0.2045 4153 RANDOM
Rwork0.1614 --
all0.1614 87648 -
obs0.1614 87648 -
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9414 0 180 215 9809
LS refinement shellResolution: 2.1→2.18 Å / Num. reflection Rfree: 334

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