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- PDB-1gti: MODIFIED GLUTATHIONE S-TRANSFERASE (PI) COMPLEXED WITH S (P-NITRO... -

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Basic information

Entry
Database: PDB / ID: 1gti
TitleMODIFIED GLUTATHIONE S-TRANSFERASE (PI) COMPLEXED WITH S (P-NITROBENZYL)GLUTATHIONE
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / GLUTATHIONE
Function / homology
Function and homology information


negative regulation of neutrophil aggregation / Paracetamol ADME / Glutathione conjugation / Detoxification of Reactive Oxygen Species / negative regulation of leukocyte proliferation / common myeloid progenitor cell proliferation / cellular response to cell-matrix adhesion / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / response to L-ascorbic acid ...negative regulation of neutrophil aggregation / Paracetamol ADME / Glutathione conjugation / Detoxification of Reactive Oxygen Species / negative regulation of leukocyte proliferation / common myeloid progenitor cell proliferation / cellular response to cell-matrix adhesion / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / response to L-ascorbic acid / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / oligodendrocyte development / negative regulation of stress-activated MAPK cascade / negative regulation of JNK cascade / prostaglandin metabolic process / cellular response to glucocorticoid stimulus / negative regulation of interleukin-1 beta production / regulation of stress-activated MAPK cascade / negative regulation of acute inflammatory response / glutathione transferase / glutathione transferase activity / negative regulation of tumor necrosis factor production / protein serine/threonine kinase inhibitor activity / animal organ regeneration / response to amino acid / regulation of ERK1 and ERK2 cascade / negative regulation of fibroblast proliferation / positive regulation of superoxide anion generation / Neutrophil degranulation / negative regulation of canonical NF-kappaB signal transduction / glutathione metabolic process / xenobiotic metabolic process / cellular response to epidermal growth factor stimulus / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / response to nutrient levels / negative regulation of ERK1 and ERK2 cascade / response to toxic substance / cellular response to insulin stimulus / response to estradiol / cellular response to lipopolysaccharide / response to ethanol / inflammatory response / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleus / cytosol
Similarity search - Function
Glutathione S-transferase, Pi class / 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, Pi class / 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
S-(P-NITROBENZYL)GLUTATHIONE / Glutathione S-transferase P 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsVega, M.C. / Coll, M.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: The three-dimensional structure of Cys-47-modified mouse liver glutathione S-transferase P1-1. Carboxymethylation dramatically decreases the affinity for glutathione and is associated with a ...Title: The three-dimensional structure of Cys-47-modified mouse liver glutathione S-transferase P1-1. Carboxymethylation dramatically decreases the affinity for glutathione and is associated with a loss of electron density in the alphaB-310B region.
Authors: Vega, M.C. / Walsh, S.B. / Mantle, T.J. / Coll, M.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Molecular Structure at 1.8 A 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.
History
DepositionJan 9, 1998Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / struct_conn / struct_ref_seq_dif / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)144,02712
Polymers141,3726
Non-polymers2,6556
Water00
1
C: GLUTATHIONE S-TRANSFERASE
D: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0094
Polymers47,1242
Non-polymers8852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-26 kcal/mol
Surface area18680 Å2
MethodPISA
2
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0094
Polymers47,1242
Non-polymers8852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-24 kcal/mol
Surface area18510 Å2
MethodPISA
3
E: GLUTATHIONE S-TRANSFERASE
F: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0094
Polymers47,1242
Non-polymers8852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-23 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.450, 132.690, 214.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.999925, 0.000245, -0.012233), (-0.009545, -0.641091, 0.767405), (-0.007655, 0.767465, 0.641046)21.475, 0.9417, -0.1857
2given(-0.99962, 0.006949, -0.026685), (-0.02495, -0.639962, 0.768002), (-0.011741, 0.768375, 0.639892)20.4481, 61.7159, -9.2908
3given(0.999909, -0.010656, 0.008308), (0.010674, 0.999941, -0.002044), (-0.008286, 0.002132, 0.999963)0.639, -45.9964, 40.8751
4given(-0.641597, -0.766897, -0.014906), (0.485318, -0.420919, 0.766351), (-0.593987, 0.484454, 0.642249)79.7102, 31.2915, -26.0391
5given(0.639958, 0.768409, 0.001011), (-0.768169, 0.639724, 0.025866), (0.019229, -0.01733, 0.999665)-58.287, -39.8321, 7.2378

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Components

#1: Protein
GLUTATHIONE S-TRANSFERASE / GST


Mass: 23562.000 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: CARBOXYMETHYLATION IN RESIDUE CYS 47 / Source: (natural) Mus musculus (house mouse) / Cellular location: CYTOPLASM / Organ: LIVER / References: UniProt: P19157, glutathione transferase
#2: Chemical
ChemComp-GTB / S-(P-NITROBENZYL)GLUTATHIONE


Mass: 442.444 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H22N4O8S

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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: 3.15 Å3/Da / Density % sol: 60.84 %
Crystal growpH: 6.4 / Details: pH 6.4
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.5 mg/mlprotein1drop
23.3 %PEG80001drop
30.017 MMOPS1drop
40.033 Mammonium sulfate1drop
50.033 MMES1drop
610 %PEG80001reservoir
750 mMMOPS1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorDetector: IMAGE PLATE / Date: Jul 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 3→8 Å / Num. obs: 23892 / % possible obs: 80 % / Observed criterion σ(I): 1.5 / Rsym value: 0.12 / Net I/σ(I): 3.7
Reflection shellResolution: 3→3.2 Å / Rmerge(I) obs: 0.2 / Rsym value: 0.2 / % possible all: 56
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 28900 / % possible obs: 79.4 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.13
Reflection shell
*PLUS
% possible obs: 73.4 %

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GLQ

1glq


Resolution: 3→8 Å / σ(F): 1.5
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1155 5 %RANDOM
Rwork0.246 ---
obs0.246 23892 52.5 %-
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9948 0 180 0 10128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.189
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.63
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.931
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 NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11RESTRAINTSX-RAY DIFFRACTION0.0371300
22X-RAY DIFFRACTION0.0173200
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19_G.PEP
X-RAY DIFFRACTION3TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.63
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.931

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