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- PDB-6ji6: Crystal structure of glutathione S-transferase complexed and modi... -

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Basic information

Entry
Database: PDB / ID: 6ji6
TitleCrystal structure of glutathione S-transferase complexed and modified with glutathione
ComponentsGlutathione S-transferase class-mu 26 kDa isozyme
KeywordsTRANSFERASE / glutathione S-transferase
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
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 / 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, 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
ACETATE ION / GLUTATHIONE / Glutathione S-transferase class-mu 26 kDa isozyme
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsOkajima, T. / Arai, R.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16K05841 Japan
Japan Society for the Promotion of Science16H00761 Japan
CitationJournal: To Be Published
Title: Crystal structure of glutathione S-transferase complexed and modified with glutathione
Authors: Okajima, T. / Arai, R.
History
DepositionFeb 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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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)27,8998
Polymers26,4301
Non-polymers1,4707
Water6,756375
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)55,79816
Polymers52,8592
Non-polymers2,93914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7880 Å2
ΔGint-44 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.708, 93.708, 57.609
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-686-

HOH

21A-695-

HOH

31A-706-

HOH

41A-717-

HOH

51A-731-

HOH

61A-736-

HOH

71A-740-

HOH

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Components

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


Mass: 26429.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Plasmid: pGEX-4T-3-SY3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P08515, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.51 Å3/Da / Density % sol: 51.03 % / Description: Rod-like crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris, 0.4M Ammonium acetate, 26% w/v PEG 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Feb 27, 2018
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 40217 / % possible obs: 97.2 % / Redundancy: 22.3 % / Biso Wilson estimate: 22.4 Å2 / CC1/2: 1 / Rpim(I) all: 0.039 / Rrim(I) all: 0.192 / Rsym value: 0.188 / Net I/σ(I): 16.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4070 / CC1/2: 0.858 / Rpim(I) all: 0.215 / Rrim(I) all: 0.742 / Rsym value: 0.708 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UA5

1ua5


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.491 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 1999 5 %RANDOM
Rwork0.1908 ---
obs0.19242 37812 96.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 96 375 2241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191953
X-RAY DIFFRACTIONr_bond_other_d0.0050.021851
X-RAY DIFFRACTIONr_angle_refined_deg1.4672.0242641
X-RAY DIFFRACTIONr_angle_other_deg0.84434294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3945228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38324.02387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24215342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.122159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212170
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02443
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9181.356879
X-RAY DIFFRACTIONr_mcbond_other0.9121.35875
X-RAY DIFFRACTIONr_mcangle_it1.5232.0241098
X-RAY DIFFRACTIONr_mcangle_other1.5232.0261099
X-RAY DIFFRACTIONr_scbond_it1.4141.6261074
X-RAY DIFFRACTIONr_scbond_other1.4131.6271075
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2682.361538
X-RAY DIFFRACTIONr_long_range_B_refined5.53113.9112691
X-RAY DIFFRACTIONr_long_range_B_other5.53113.9162692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 131 -
Rwork0.283 2500 -
obs--86.92 %

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