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- PDB-2ljr: GLUTATHIONE TRANSFERASE APO-FORM FROM HUMAN -

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Basic information

Entry
Database: PDB / ID: 2ljr
TitleGLUTATHIONE TRANSFERASE APO-FORM FROM HUMAN
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


Glutathione conjugation / glutathione transferase / glutathione transferase activity / glutathione metabolic process / extracellular exosome / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Glutathione S-transferase Theta, N-terminal / Glutathione S-transferase Theta, C-terminal / : / 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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferase Theta, N-terminal / Glutathione S-transferase Theta, C-terminal / : / 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 / 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 S-transferase theta-2B / Glutathione S-transferase theta-2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsRossjohn, J. / Mckinstry, W.J. / Oakley, A.J. / Verger, D. / Flanagan, J. / Chelvanayagam, G. / Tan, K.L. / Board, P.G. / Parker, M.W.
CitationJournal: Structure / Year: 1998
Title: Human theta class glutathione transferase: the crystal structure reveals a sulfate-binding pocket within a buried active site.
Authors: Rossjohn, J. / McKinstry, W.J. / Oakley, A.J. / Verger, D. / Flanagan, J. / Chelvanayagam, G. / Tan, K.L. / Board, P.G. / Parker, M.W.
History
DepositionMar 8, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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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


Theoretical massNumber of molelcules
Total (without water)55,0762
Polymers55,0762
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-18 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.620, 93.620, 120.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.197043, 0.980821, -0.010087), (0.980231, 0.197028, 0.000779), (0.002713, -0.00964, -1.00031)
Vector: -52.93217, 43.54286, 21.06538)

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE / HGST T2-2


Mass: 27537.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: APO FORM / Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli)
References: UniProt: P30712, UniProt: P0CG30*PLUS, glutathione transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTWO WATER MOLECULES HAVE BEEN MODELLED IN THE ACTIVE SITE: ONE PER MONOMER. IT IS BELIEVED, FROM ...TWO WATER MOLECULES HAVE BEEN MODELLED IN THE ACTIVE SITE: ONE PER MONOMER. IT IS BELIEVED, FROM THE STRONG FEATURES IN THE FO - FC MAPS, THAT THESE "WATER" MOLECULES ACTUALLY REPRESENT A SULFATE OR PHOSPHATE ANION. THE LOW RESOLUTION LIMITS US TO TO MODEL THESE FEATURES AS A WATER MOLECULE ONLY HOWEVER. THE LOCATION OF THIS PUTATIVE SULFATE BINDING SITE WAS VALIDATED VIA A VANADATE SOAK (SEE PAPER), AND VIA THE MENAPHTHYL SULFATE COMPLEX (PDB CODE: 3LJR)

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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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal grow
*PLUS
Temperature: 277 or 295 K / pH: 7 / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.76 mg/mlprotein1drop
210 mMsodium phosphate1drop
31 mMbeta-mercaptoethanol1drop
415 %PEG40001reservoir
52 %ethanol1reservoir
6100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorDetector: FILM / Date: Dec 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→15 Å / Num. obs: 9362 / % possible obs: 89.2 % / Redundancy: 1.9 % / Rsym value: 0.109 / Net I/σ(I): 7.9
Reflection shellResolution: 3.2→3.3 Å / Mean I/σ(I) obs: 2 / % possible all: 87.2
Reflection
*PLUS
Num. measured all: 17711 / Rmerge(I) obs: 0.109
Reflection shell
*PLUS
% possible obs: 87.2 %

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementResolution: 3.2→15 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.291 -10 %RANDOM
Rwork0.2 ---
obs0.2 9362 89.2 %-
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 0 2 3882
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.7
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
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.7

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