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- PDB-2j9h: Crystal structure of human glutathione-S-transferase P1-1 cys-fre... -

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Basic information

Entry
Database: PDB / ID: 2j9h
TitleCrystal structure of human glutathione-S-transferase P1-1 cys-free mutant in complex with S-hexylglutathione at 2.4 A resolution
ComponentsGLUTATHIONE S-TRANSFERASE P
KeywordsTRANSFERASE / P1-1 / GLUTATHIONE / POLYMORPHISM / GLUTATHIONE TRANSFERASE
Function / homology
Function and homology information


nitric oxide storage / S-nitrosoglutathione binding / kinase regulator activity / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process ...nitric oxide storage / S-nitrosoglutathione binding / kinase regulator activity / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / negative regulation of JUN kinase activity / nitric oxide binding / linoleic acid metabolic process / negative regulation of leukocyte proliferation / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / Paracetamol ADME / glutathione peroxidase activity / 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 MAPK cascade / Detoxification of Reactive Oxygen Species / glutathione transferase / negative regulation of acute inflammatory response / glutathione transferase activity / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / glutathione metabolic process / negative regulation of canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / xenobiotic metabolic process / response to reactive oxygen species / regulation of ERK1 and ERK2 cascade / negative regulation of MAP kinase activity / positive regulation of superoxide anion generation / central nervous system development / fatty acid binding / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / secretory granule lumen / cellular response to lipopolysaccharide / 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 / 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, 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 / 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-HEXYLGLUTATHIONE / Glutathione S-transferase P
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTars, K. / Hegazy, U.M. / Hellman, U. / Mannervik, B.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Modulating Catalytic Activity by Unnatural Amino Acid Residues in a Gsh-Binding Loop of Gst P1-1.
Authors: Hegazy, U.M. / Tars, K. / Hellman, U. / Mannervik, B.
History
DepositionNov 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
B: GLUTATHIONE S-TRANSFERASE P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0864
Polymers46,3012
Non-polymers7852
Water81145
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-23.3 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.566, 59.566, 238.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999457, 0.002414, 0.032846), (-0.029422, -0.513625, -0.857509), (0.0148, -0.858011, 0.513418)
Vector: 43.889, 3.516, 1.637)

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE P / GLUTATHIONE-S-TRANSFERASE P1-1 / GST CLASS-PI / GSTP1-1


Mass: 23150.311 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL-1 BLUE / References: UniProt: P09211, glutathione transferase
#2: Chemical ChemComp-GTX / S-HEXYLGLUTATHIONE


Mass: 392.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 15 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 48 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, CYS 15 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 48 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 102 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 170 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 15 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 48 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 102 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 170 TO SER

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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: 2.24 Å3/Da / Density % sol: 44.62 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.4
Details: SITTING DROP VAPOUR TECHNIQUE, 1 MICROLITRE OF PROTEIN AT 10 MG/ML IN 20 MM TRIS-HCL, PH 8.0 CONTAINING 5MM S-HEXYLGLUTATHIONE WAS MIXED WITH 1 MICROLITRE OF RESERVOIR SOLUTION, COMPOSED OF ...Details: SITTING DROP VAPOUR TECHNIQUE, 1 MICROLITRE OF PROTEIN AT 10 MG/ML IN 20 MM TRIS-HCL, PH 8.0 CONTAINING 5MM S-HEXYLGLUTATHIONE WAS MIXED WITH 1 MICROLITRE OF RESERVOIR SOLUTION, COMPOSED OF 1.5M AMMONIUM SULFATE AND 100MM SODIUM CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.042
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.042 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 16119 / % possible obs: 90 % / Observed criterion σ(I): 2.4 / Redundancy: 6.5 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.8
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.4 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 9GSS

9gss


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.888 / SU B: 12.479 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R: 0.868 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31 808 5 %RANDOM
Rwork0.25 ---
obs0.253 15269 90.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 52 45 3369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223392
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.50724598
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg65416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.8924.8150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.97115562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1921516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022570
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.21609
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22272
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2147
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5411.52146
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95423324
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.40731433
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1064.51274
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.481 69 -
Rwork0.313 1175 -
obs--99.28 %

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