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- PDB-1c72: TYR115, GLN165 AND TRP209 CONTRIBUTE TO THE 1,2-EPOXY-3-(P-NITROP... -

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Basic information

Entry
Database: PDB / ID: 1c72
TitleTYR115, GLN165 AND TRP209 CONTRIBUTE TO THE 1,2-EPOXY-3-(P-NITROPHENOXY)PROPANE CONJUGATING ACTIVITIES OF GLUTATHIONE S-TRANSFERASE CGSTM1-1
ComponentsPROTEIN (GLUTATHIONE S-TRANSFERASE)
KeywordsTRANSFERASE / GLUTATHIONE S-TRANSFERASE / 1 / 2-EPOXY-3-(P-NITROPHENOXY)PROPANE / EPOXIDASE ACTIVITY / STEADY-STATE KINETICS
Function / homology
Function and homology information


Glutathione conjugation / Biosynthesis of maresin conjugates in tissue regeneration (MCTR) / Azathioprine ADME / Paracetamol ADME / glutathione transferase / glutathione transferase activity / glutathione metabolic process / lipid metabolic process / identical protein binding / cytoplasm
Similarity search - Function
Glutathione S-transferase, Mu class / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferase, Mu class / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / 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
Chem-EPY / Glutathione S-transferase 2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChern, M.K. / Wu, T.C. / Hsieh, C.H. / Chou, C.C. / Liu, L.F. / Kuan, I.C. / Yeh, Y.H. / Hsiao, C.D. / Tam, M.F.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Tyr115, gln165 and trp209 contribute to the 1, 2-epoxy-3-(p-nitrophenoxy)propane-conjugating activity of glutathione S-transferase cGSTM1-1.
Authors: Chern, M.K. / Wu, T.C. / Hsieh, C.H. / Chou, C.C. / Liu, L.F. / Kuan, I.C. / Yeh, Y.H. / Hsiao, C.D. / Tam, M.F.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: The Three-Dimensional Structure of an Avian Class-Mu Glutathione S-Transferase, cGSTM1-1 at 1.94A Resolution
Authors: Sun, Y.J. / Kuan, I.C. / Tam, M.F. / Hsiao, C.D.
History
DepositionFeb 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / 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 / _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: PROTEIN (GLUTATHIONE S-TRANSFERASE)
B: PROTEIN (GLUTATHIONE S-TRANSFERASE)
C: PROTEIN (GLUTATHIONE S-TRANSFERASE)
D: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1298
Polymers103,1194
Non-polymers2,0104
Water2,846158
1
A: PROTEIN (GLUTATHIONE S-TRANSFERASE)
B: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5644
Polymers51,5592
Non-polymers1,0052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PROTEIN (GLUTATHIONE S-TRANSFERASE)
D: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5644
Polymers51,5592
Non-polymers1,0052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.600, 136.650, 125.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
PROTEIN (GLUTATHIONE S-TRANSFERASE) / GSTS


Mass: 25779.650 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: 1,2-EPOXY-3-(P-NITROPHENOXY)PROPANE / Source: (gene. exp.) Gallus gallus (chicken) / Organ: LIVER / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P20136, glutathione transferase
#2: Chemical
ChemComp-EPY / 1-HYDROXY-2-S-GLUTATHIONYL-3-PARA-NITROPHENOXY-PROPANE


Mass: 502.496 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H26N4O10S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 mg/mlprotein1drop
240 mMGS-EPNP1drop
350 mMTris-H2SO41drop
40.1 Msodium acetate1reservoir
50.3 Mammonium acetate1reservoir
626 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 15, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→31 Å / Num. obs: 25597 / % possible obs: 91.9 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 37 Å2 / Rsym value: 0.09 / Net I/σ(I): 14.6
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.17 / Rsym value: 0.317 / % possible all: 89.2
Reflection
*PLUS
% possible obs: 86.6 % / Num. measured all: 66453 / Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GSU

1gsu


Resolution: 2.8→31 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2163 9.9 %RANDOM
Rwork0.19 ---
obs0.19 21857 86.6 %-
Displacement parametersBiso mean: 31.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.28 Å
Luzzati d res low-3.5 Å
Luzzati sigma a0.5 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.8→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7200 0 136 158 7494
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.68
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.41.5
X-RAY DIFFRACTIONx_mcangle_it6.392
X-RAY DIFFRACTIONx_scbond_it4.662
X-RAY DIFFRACTIONx_scangle_it6.552.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 267 9.8 %
Rwork0.246 2468 -
obs--73.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TIP3P.PARAMETERTIP3P.TOPOLOGY
X-RAY DIFFRACTION3GSH-EPNP.PARGSH-EPNP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 31 Å / σ(F): 2 / % reflection Rfree: 9.9 % / Rfactor obs: 0.19 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.68
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.35 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.246

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