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- PDB-2pmt: GLUTATHIONE TRANSFERASE FROM PROTEUS MIRABILIS -

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Basic information

Entry
Database: PDB / ID: 2pmt
TitleGLUTATHIONE TRANSFERASE FROM PROTEUS MIRABILIS
ComponentsGLUTATHIONE TRANSFERASE
KeywordsTRANSFERASE / GLUTATHIONE-CONJUGATING / A PUTATIVE OXIDOREDUCTASE
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / cytoplasm
Similarity search - Function
Glutathione S-transferase, N-terminal domain / 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, N-terminal domain / 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 / Glutathione S-transferase GST-6.0
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRossjohn, J. / Polekhina, G. / Feil, S.C. / Allocati, N. / Masulli, M. / Diilio, C. / Parker, M.W.
CitationJournal: Structure / Year: 1998
Title: A mixed disulfide bond in bacterial glutathione transferase: functional and evolutionary implications.
Authors: Rossjohn, J. / Polekhina, G. / Feil, S.C. / Allocati, N. / Masulli, M. / De Illio, C. / Parker, M.W.
History
DepositionApr 28, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 18, 2012Group: Derived calculations / Non-polymer description
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _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 TRANSFERASE
B: GLUTATHIONE TRANSFERASE
C: GLUTATHIONE TRANSFERASE
D: GLUTATHIONE TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7548
Polymers91,5254
Non-polymers1,2294
Water00
1
A: GLUTATHIONE TRANSFERASE
B: GLUTATHIONE TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3774
Polymers45,7622
Non-polymers6152
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-23 kcal/mol
Surface area16590 Å2
MethodPISA
2
C: GLUTATHIONE TRANSFERASE
D: GLUTATHIONE TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3774
Polymers45,7622
Non-polymers6152
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-23 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.885, 90.885, 117.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.611254, 0.655958, -0.442817), (0.661327, -0.730692, -0.169515), (-0.434758, -0.189231, -0.880442)-29.26124, 84.86531, 20.01581
2given(-0.863623, 0.490368, 0.117027), (0.48407, 0.741749, 0.464203), (0.140825, 0.457545, -0.877964)-13.86151, -18.71287, 85.06853
3given(-0.118536, 0.992918, -0.007898), (0.992935, 0.118574, 0.004433), (0.005338, -0.007317, -0.999959)-39.6834, 40.50508, 63.35114

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Components

#1: Protein
GLUTATHIONE TRANSFERASE / PMGST / GST B1-1


Mass: 22881.244 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Cellular location: PERIPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P15214, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S

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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: 2.65 Å3/Da / Density % sol: 54 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
222-28 %PEG80001reservoir
3100 mMHEPES1reservoir
410 mMreduced DSH1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9
DetectorType: MARRESEARCH / Date: Aug 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 22464 / % possible obs: 85.8 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.147 / Net I/σ(I): 7.8
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.382 / % possible all: 90
Reflection
*PLUS
Num. measured all: 60878 / Rmerge(I) obs: 0.147
Reflection shell
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.382

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→20 Å / Data cutoff high absF: 10000000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 -5 %RANDOM
Rwork0.2086 ---
obs0.2086 23008 85.8 %-
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6380 0 80 0 6460
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2438
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_deg25.9
X-RAY DIFFRACTIONx_improper_angle_deg0.7

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