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- PDB-4wr4: Crystal Structure of GST Mutated with Halogenated Tyrosine (7bGST-1) -

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Basic information

Entry
Database: PDB / ID: 4wr4
TitleCrystal Structure of GST Mutated with Halogenated Tyrosine (7bGST-1)
ComponentsGlutathione S-transferase class-mu 26 kDa isozyme
KeywordsTRANSFERASE / THEMOSTABILIZED STRUCTURE / HOMODIMERIC / TWO DOMAINS / ALFA/BETA / ALFA / DETOXIFICATION / XENOBIOTIC COMPOUNDS / GUTATHIONE / 7 SPECFIC SITES / CYTOPLASMIC
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
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 / 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 / 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 / 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
GLUTATHIONE / Glutathione S-transferase class-mu 26 kDa isozyme
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAkasaka, R. / Kawazoe, M. / Tomabechi, Y. / Ohtake, K. / Itagaki, T. / Takemoto, C. / Shirouzu, M. / Yokoyama, S. / Sakamoto, K.
CitationJournal: Sci Rep / Year: 2015
Title: Protein stabilization utilizing a redefined codon
Authors: Ohtake, K. / Yamaguchi, A. / Mukai, T. / Kashimura, H. / Hirano, N. / Haruki, M. / Kohashi, S. / Yamagishi, K. / Murayama, K. / Tomabechi, Y. / Itagaki, T. / Akasaka, R. / Kawazoe, M. / ...Authors: Ohtake, K. / Yamaguchi, A. / Mukai, T. / Kashimura, H. / Hirano, N. / Haruki, M. / Kohashi, S. / Yamagishi, K. / Murayama, K. / Tomabechi, Y. / Itagaki, T. / Akasaka, R. / Kawazoe, M. / Takemoto, C. / Shirouzu, M. / Yokoyama, S. / Sakamoto, K.
History
DepositionOct 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_oper_list / reflns_shell
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.Rmerge_I_obs
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase class-mu 26 kDa isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1874
Polymers28,6881
Non-polymers4993
Water2,450136
1
A: Glutathione S-transferase class-mu 26 kDa isozyme
hetero molecules

A: Glutathione S-transferase class-mu 26 kDa isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3748
Polymers57,3762
Non-polymers9996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area4570 Å2
ΔGint-59 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.850, 63.850, 225.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-452-

HOH

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Components

#1: Protein Glutathione S-transferase class-mu 26 kDa isozyme / 7bGST-1 / GST 26 / Sj26 antigen / SjGST


Mass: 28687.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Plasmid: PBR322 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08515, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M TRI-SODIUM CITRATE, 1.3M AMMONIUM SULFATE, 0.2M LITHIUM SULFATE

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 8, 2013
RadiationMonochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→44.508 Å / Num. all: 36905 / Num. obs: 36508 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 13.81 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 17.2
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 2.13 / Mean I/σ(I) obs: 1.31 / % possible all: 99.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX(PHENIX.REFINE: 1.8.3_1479)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UA5

1ua5


Resolution: 1.6→44.508 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 1825 5 %
Rwork0.191 --
obs0.192 36483 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.86 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 30 136 1968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011879
X-RAY DIFFRACTIONf_angle_d1.3772542
X-RAY DIFFRACTIONf_dihedral_angle_d13.122728
X-RAY DIFFRACTIONf_chiral_restr0.069261
X-RAY DIFFRACTIONf_plane_restr0.008319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6013-1.64460.31651360.30722582X-RAY DIFFRACTION99
1.6446-1.69290.2791390.2752626X-RAY DIFFRACTION100
1.6929-1.74760.27911370.24832614X-RAY DIFFRACTION100
1.7476-1.81010.28211380.23442629X-RAY DIFFRACTION100
1.8101-1.88250.27621400.22072664X-RAY DIFFRACTION100
1.8825-1.96820.24351390.20562625X-RAY DIFFRACTION100
1.9682-2.0720.22631390.18852655X-RAY DIFFRACTION100
2.072-2.20180.21011400.18212660X-RAY DIFFRACTION99
2.2018-2.37180.20221400.1772658X-RAY DIFFRACTION99
2.3718-2.61040.22771410.18182671X-RAY DIFFRACTION99
2.6104-2.98810.20891420.19412695X-RAY DIFFRACTION98
2.9881-3.76440.22081420.18292708X-RAY DIFFRACTION97
3.7644-44.52550.1991520.17032871X-RAY DIFFRACTION96

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