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- PDB-3o76: 1.8 Angstroms molecular structure of mouse liver glutathione S-tr... -

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Basic information

Entry
Database: PDB / ID: 3o76
Title1.8 Angstroms molecular structure of mouse liver glutathione S-transferase mutant C47A complexed with S-(P-nitrobenzyl)glutathione
ComponentsGlutathione S-transferase P 1
KeywordsTRANSFERASE / TRANSFERASE(GLUTATHIONE)
Function / homology
Function and homology information


cellular response to cell-matrix adhesion / negative regulation of neutrophil aggregation / negative regulation of peroxidase activity / Paracetamol ADME / Glutathione conjugation / negative regulation of smooth muscle cell chemotaxis / Detoxification of Reactive Oxygen Species / kinase regulator activity / negative regulation of leukocyte proliferation / response to L-ascorbic acid ...cellular response to cell-matrix adhesion / negative regulation of neutrophil aggregation / negative regulation of peroxidase activity / Paracetamol ADME / Glutathione conjugation / negative regulation of smooth muscle cell chemotaxis / Detoxification of Reactive Oxygen Species / kinase regulator activity / negative regulation of leukocyte proliferation / response to L-ascorbic acid / common myeloid progenitor cell proliferation / organic cyclic compound binding / glutathione derivative biosynthetic process / hepoxilin biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / oligodendrocyte development / negative regulation of JUN kinase activity / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / cellular response to glucocorticoid stimulus / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / regulation of stress-activated MAPK cascade / prostaglandin metabolic process / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of acute inflammatory response / glutathione transferase / negative regulation of tumor necrosis factor production / glutathione transferase activity / toxic substance binding / response to amino acid / animal organ regeneration / negative regulation of fibroblast proliferation / negative regulation of canonical NF-kappaB signal transduction / cellular response to epidermal growth factor stimulus / Neutrophil degranulation / xenobiotic metabolic process / response to nutrient levels / glutathione metabolic process / regulation of ERK1 and ERK2 cascade / positive regulation of superoxide anion generation / negative regulation of MAP kinase activity / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / 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 / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / mitochondrion / nucleus / plasma membrane / cytoplasm / 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-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: 1.77 Å
AuthorsCanals, A. / Coll, M.
CitationJournal: Febs J. / Year: 2011
Title: Site-directed mutagenesis of mouse glutathione transferase P1-1 unlocks masked cooperativity, introduces a novel mechanism for 'ping pong' kinetic behaviour, and provides further structural ...Title: Site-directed mutagenesis of mouse glutathione transferase P1-1 unlocks masked cooperativity, introduces a novel mechanism for 'ping pong' kinetic behaviour, and provides further structural evidence for participation of a water molecule in proton abstraction from glutathione.
Authors: McManus, G. / Costa, M. / Canals, A. / Coll, M. / Mantle, T.J.
History
DepositionJul 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / diffrn_source / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _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 P 1
B: Glutathione S-transferase P 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8294
Polymers46,9442
Non-polymers8852
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-23 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.612, 60.612, 233.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Glutathione S-transferase P 1 / Gst P1 / GST YF-YF / GST-piB / GST class-pi / Preadipocyte growth factor


Mass: 23471.898 Da / Num. of mol.: 2 / Mutation: C47A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gstp1, Gstpib / Production host: Escherichia coli (E. coli) / References: UniProt: P19157, glutathione transferase
#2: Chemical ChemComp-GTB / S-(P-NITROBENZYL)GLUTATHIONE


Mass: 442.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H22N4O8S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 293 K / pH: 4
Details: 20% PEG 6000, 0.1 M sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9114
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 25, 1999
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9114 Å / Relative weight: 1
ReflectionResolution: 1.77→20 Å / Num. obs: 43759 / % possible obs: 98.2 % / Observed criterion σ(I): 2
Reflection shellResolution: 1.77→1.87 Å / % possible all: 88

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GLQ

1glq


Resolution: 1.77→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.464 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 3078 7.2 %RANDOM
Rwork0.197 ---
obs0.199 39924 98.5 %-
all-39924 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.77→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 60 409 3775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223440
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1421.9954658
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7565416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4324.43158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55515580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8531520
X-RAY DIFFRACTIONr_chiral_restr0.0770.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022642
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.21717
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22340
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2358
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4461.52153
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.67123334
X-RAY DIFFRACTIONr_scbond_it1.19231482
X-RAY DIFFRACTIONr_scangle_it1.7864.51324
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 185 -
Rwork0.252 2288 -
obs--78.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5664-0.3432-0.5661.30270.14732.1656-0.11660.1911-0.10540.2045-0.05130.24960.1504-0.43480.168-0.0449-0.03550.0932-0.0107-0.03790.015357.15532.043796.7905
20.93040.0247-0.77712.08260.11831.00310.1361-0.10710.05070.5465-0.02710.0092-0.04480.2263-0.10890.1194-0.01970.0249-0.0762-0.015-0.082175.120844.9657108.3586
34.298610.5871-7.999734.1302-27.233421.9283-0.53540.51630.4210.54341.19081.25060.1972-1.1322-0.65530.13690.02360.2114-0.06930.0469-0.003160.740725.8125108.6218
420.9923-3.3289-2.67560.8710.79760.74710.2067-0.63130.71420.5866-0.1893-0.2926-0.0385-0.2773-0.01750.18680.01180.1414-0.10730.0203-0.038563.497751.2304110.0951
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 209
2X-RAY DIFFRACTION2B1 - 209
3X-RAY DIFFRACTION3A210
4X-RAY DIFFRACTION4B210

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