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- PDB-2oac: Mouse C14A Glutathione-S-Transferase Mutant in Complex with S-(p-... -

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Basic information

Entry
Database: PDB / ID: 2oac
TitleMouse C14A Glutathione-S-Transferase Mutant in Complex with S-(p-nitrobenzyl) Glutathione
ComponentsGlutathione S-transferase P 1
KeywordsTRANSFERASE / mutant protein and ligand complex
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 / S-nitrosoglutathione binding / kinase regulator activity / 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 / S-nitrosoglutathione binding / kinase regulator activity / response to L-ascorbic acid / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / organic cyclic compound binding / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / oligodendrocyte development / negative regulation of nitric-oxide synthase biosynthetic process / negative regulation of JUN kinase activity / linoleic acid metabolic process / negative regulation of leukocyte proliferation / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / glutathione peroxidase activity / 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 / glutathione transferase / negative regulation of acute inflammatory response / glutathione transferase activity / negative regulation of tumor necrosis factor production / toxic substance binding / response to amino acid / animal organ regeneration / glutathione metabolic process / negative regulation of canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / cellular response to epidermal growth factor stimulus / Neutrophil degranulation / xenobiotic metabolic process / response to reactive oxygen species / response to nutrient levels / regulation of ERK1 and ERK2 cascade / negative regulation of MAP kinase activity / positive regulation of superoxide anion generation / fatty acid binding / 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 / response to ethanol / cellular response to lipopolysaccharide / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / mitochondrion / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKyrieleis, O.J. / McManus, G. / Mantle, T.J. / Khan, A.R.
CitationJournal: TO BE PUBLISHED
Title: Structural and Kinetic Analyses of Glutathione S-Transferase Mutants
Authors: Kyrieleis, O.J. / McManus, G. / Mantle, T.J. / Khan, A.R.
History
DepositionDec 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-22 kcal/mol
Surface area17390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.360, 77.140, 101.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 23471.898 Da / Num. of mol.: 2 / Mutation: C14A
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 / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.35 Å3/Da / Density % sol: 47.58 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 3, 2006 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 3.1 % / Av σ(I) over netI: 21.8 / Number: 60637 / Rmerge(I) obs: 0.06 / Χ2: 1.53 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 19607 / % possible obs: 84.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.74507610.0340.9433
3.764.7481.910.0381.0543.2
3.293.7682.610.0491.1793.2
2.993.2984.410.0651.3783.1
2.772.9984.910.0791.5733.1
2.612.7786.510.0971.553.1
2.482.6187.410.1111.7883
2.372.4886.510.1411.7283.1
2.282.3788.710.1752.1053.1
2.22.2887.510.2051.933.1
ReflectionResolution: 2.2→50 Å / Num. all: 23245 / Num. obs: 19354 / % possible obs: 84.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Χ2: 1.526 / Net I/σ(I): 21.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.205 / Num. unique all: 1999 / Χ2: 1.93 / % possible all: 87.5

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Processing

Software
NameVersionClassificationNB
CNSrefinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
HKL-2000data reduction
AMoREphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BAY

1bay


Resolution: 2.2→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 946 4.1 %random
Rwork0.22 ---
all0.239 23245 --
obs0.228 19354 84.6 %-
Solvent computationBsol: 39.402 Å2
Displacement parametersBiso mean: 26.73 Å2
Baniso -1Baniso -2Baniso -3
1--6.411 Å20 Å20 Å2
2--1.091 Å20 Å2
3---5.32 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 60 181 3547
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.207
X-RAY DIFFRACTIONc_mcbond_it1.1661.5
X-RAY DIFFRACTIONc_scbond_it1.8442
X-RAY DIFFRACTIONc_mcangle_it1.7642
X-RAY DIFFRACTIONc_scangle_it2.5352.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5gtb.paramgtb.top

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