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- PDB-3hjm: Crystal structure of human Glutathione Transferase Pi Y108V mutant -

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Basic information

Entry
Database: PDB / ID: 3hjm
TitleCrystal structure of human Glutathione Transferase Pi Y108V mutant
ComponentsGlutathione S-transferase P
KeywordsTRANSFERASE / GLUTATHIONE / DETOXIFICATION / MUTANT / Polymorphism
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
CARBONATE ION / PHOSPHATE ION / Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 22, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase P
B: Glutathione S-transferase P
C: Glutathione S-transferase P
D: Glutathione S-transferase P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,01821
Polymers92,7304
Non-polymers1,28717
Water11,187621
1
A: Glutathione S-transferase P
B: Glutathione S-transferase P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,08711
Polymers46,3652
Non-polymers7229
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-52 kcal/mol
Surface area18090 Å2
MethodPISA
2
C: Glutathione S-transferase P
D: Glutathione S-transferase P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,93110
Polymers46,3652
Non-polymers5668
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-57 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.002, 90.393, 75.981
Angle α, β, γ (deg.)90.000, 97.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 23182.527 Da / Num. of mol.: 4 / 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

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Non-polymers , 6 types, 638 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CO3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 621 / 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: 2.53 Å3/Da / Density % sol: 51.45 % / Mosaicity: 0.635 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 270mM Calcium Acetate, 20% PEG8000, 100mM MES, pH5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 15, 2008 / Details: AXCO
RadiationMonochromator: AXCO Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→54.55 Å / Num. obs: 53439 / % possible obs: 98.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 21.99 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 6.26
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.8 / Num. measured all: 34588 / Num. unique all: 7215 / Rsym value: 0.41 / % possible all: 92.1

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CSI

3csi


Resolution: 2.1→54.55 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.16 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.834 / SU B: 5.108 / SU ML: 0.135 / SU R Cruickshank DPI: 0.218 / SU Rfree: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2735 5.1 %RANDOM
Rwork0.18 ---
obs0.18 53417 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.88 Å2 / Biso mean: 21.361 Å2 / Biso min: 2.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å2-1.16 Å2
2---1.09 Å20 Å2
3---2.04 Å2
Refinement stepCycle: LAST / Resolution: 2.1→54.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6509 0 69 621 7199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226698
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9949085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.785832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.29824.865296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.993151134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0941532
X-RAY DIFFRACTIONr_chiral_restr0.0960.21017
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025048
X-RAY DIFFRACTIONr_nbd_refined0.1970.23126
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24531
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2570
X-RAY DIFFRACTIONr_metal_ion_refined0.1170.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.211
X-RAY DIFFRACTIONr_mcbond_it0.7811.54292
X-RAY DIFFRACTIONr_mcangle_it1.23626626
X-RAY DIFFRACTIONr_scbond_it2.03332773
X-RAY DIFFRACTIONr_scangle_it3.1014.52457
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 186 -
Rwork0.24 3245 -
all-3431 -
obs--86.75 %

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