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- PDB-3hkr: Crystal Structure of Glutathione Transferase Pi Y108V Mutant -

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Basic information

Entry
Database: PDB / ID: 3hkr
TitleCrystal Structure of Glutathione Transferase Pi Y108V Mutant
ComponentsGlutathione S-transferase P
KeywordsTRANSFERASE / GLUTATHIONE / DETOXIFICATION
Function / homology
Function and homology information


S-nitrosoglutathione binding / nitric oxide storage / negative regulation of leukocyte proliferation / TRAF2-GSTP1 complex / kinase regulator activity / negative regulation of biosynthetic process / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process ...S-nitrosoglutathione binding / nitric oxide storage / negative regulation of leukocyte proliferation / TRAF2-GSTP1 complex / kinase regulator activity / negative regulation of biosynthetic process / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / : / negative regulation of JUN kinase activity / linoleic acid metabolic process / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / nitric oxide binding / JUN kinase binding / glutathione peroxidase activity / Paracetamol ADME / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / prostaglandin metabolic process / regulation of stress-activated MAPK cascade / Detoxification of Reactive Oxygen Species / negative regulation of acute inflammatory response / glutathione transferase / negative regulation of tumor necrosis factor production / glutathione transferase activity / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of MAP kinase activity / negative regulation of MAPK cascade / regulation of ERK1 and ERK2 cascade / negative regulation of canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / glutathione metabolic process / xenobiotic metabolic process / positive regulation of superoxide anion generation / central nervous system development / fatty acid binding / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / cellular response to lipopolysaccharide / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / Neutrophil degranulation / negative regulation of apoptotic process / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / 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
CARBONATE ION / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsParker, L.J.
CitationJournal: Protein Sci. / Year: 2009
Title: Influence of the H-site residue 108 on human glutathione transferase P1-1 ligand binding: structure-thermodynamic relationships and thermal stability.
Authors: Quesada-Soriano, I. / Parker, L.J. / Primavera, A. / Casas-Solvas, J.M. / Vargas-Berenguel, A. / Baron, C. / Morton, C.J. / Mazzetti, A.P. / Lo Bello, M. / Parker, M.W. / Garcia-Fuentes, L.
History
DepositionMay 25, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 1.3Nov 1, 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
B: Glutathione S-transferase P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,13612
Polymers46,3652
Non-polymers77110
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-60 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.10, 90.30, 68.90
Angle α, β, γ (deg.)90.00, 98.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-452-

HOH

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Components

#1: Protein Glutathione S-transferase P / GST class-pi / GSTP1-1


Mass: 23182.527 Da / Num. of mol.: 2 / Mutation: Y108V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTP1 / Plasmid: PSE420 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: P09211, glutathione transferase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 267mM Calcium Acetate, 20% PEG8000, 100mM MES, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 12, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.74→100 Å / Num. obs: 47590 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 24.854 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.37
Reflection shellResolution: 1.74→1.84 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.9 / Num. measured obs: 33372 / Num. unique obs: 6993 / % possible all: 89.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5GSS

5gss


Resolution: 1.8→42.11 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.204 / WRfactor Rwork: 0.165 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.872 / SU B: 2.31 / SU ML: 0.074 / SU R Cruickshank DPI: 0.119 / SU Rfree: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2248 5.2 %RANDOM
Rwork0.17 ---
all0.17 ---
obs0.17 43129 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.99 Å2 / Biso mean: 19.247 Å2 / Biso min: 6.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0.05 Å2
2---0.07 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 41 490 3791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223361
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9954558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.175417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67324.865148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95615567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8181516
X-RAY DIFFRACTIONr_chiral_restr0.0880.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022530
X-RAY DIFFRACTIONr_nbd_refined0.1980.21655
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22301
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2420
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.213
X-RAY DIFFRACTIONr_mcbond_it0.8481.52147
X-RAY DIFFRACTIONr_mcangle_it1.23523321
X-RAY DIFFRACTIONr_scbond_it1.99831391
X-RAY DIFFRACTIONr_scangle_it3.044.51236
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 148 -
Rwork0.21 2956 -
all-3104 -
obs--98.17 %

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