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- PDB-3wd6: Crystal structure of Bombyx mori omega-class glutathione transfer... -

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Basic information

Entry
Database: PDB / ID: 3wd6
TitleCrystal structure of Bombyx mori omega-class glutathione transferase in complex with GSH
ComponentsOmega-class glutathione S-transferase
KeywordsTRANSFERASE / electron sharing network / glutathione binding
Function / homology
Function and homology information


glutathione dehydrogenase (ascorbate) activity / glutathione transferase activity / glutathione metabolic process / cytoplasm
Similarity search - Function
Glutathione S-transferase, omega-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 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, omega-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 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
GLUTATHIONE / IODIDE ION / : / DI(HYDROXYETHYL)ETHER / Omega-class glutathione S-transferase
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYamamoto, K. / Suzuki, M. / Higashiura, A. / Nakagawa, A.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Three-dimensional structure of a Bombyx mori Omega-class glutathione transferase.
Authors: Yamamoto, K. / Suzuki, M. / Higashiura, A. / Nakagawa, A.
History
DepositionJun 7, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Omega-class glutathione S-transferase
B: Omega-class glutathione S-transferase
C: Omega-class glutathione S-transferase
D: Omega-class glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,60224
Polymers119,3904
Non-polymers2,21220
Water5,963331
1
A: Omega-class glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4407
Polymers29,8471
Non-polymers5936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Omega-class glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2955
Polymers29,8471
Non-polymers4484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Omega-class glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4847
Polymers29,8471
Non-polymers6376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Omega-class glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3835
Polymers29,8471
Non-polymers5354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Omega-class glutathione S-transferase
hetero molecules

D: Omega-class glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,82312
Polymers59,6952
Non-polymers1,12810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area5130 Å2
ΔGint-25 kcal/mol
Surface area21400 Å2
MethodPISA
6
B: Omega-class glutathione S-transferase
C: Omega-class glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,77912
Polymers59,6952
Non-polymers1,08410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-27 kcal/mol
Surface area21120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.861, 89.894, 182.149
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Omega-class glutathione S-transferase / Uncharacterized protein


Mass: 29847.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: gsto, GSTo2 / Production host: Escherichia coli (E. coli) / References: UniProt: A8R5V3

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Non-polymers , 6 types, 351 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#6: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.6 Å3/Da / Density % sol: 52.71 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M potassium iodide, and 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorDetector: CCD
RadiationMonochromator: DXM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→32.84 Å / Num. obs: 43880 / % possible obs: 98.4 %
Reflection shellResolution: 2.5→2.64 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MERLOTphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→32.84 Å / SU ML: 0.76 / σ(F): 0.97 / Phase error: 26.1 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2564 2185 5.01 %
Rwork0.2079 --
obs0.2104 43880 99.83 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.25 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2984 Å20 Å2-0 Å2
2--2.3362 Å20 Å2
3----3.6345 Å2
Refinement stepCycle: LAST / Resolution: 2.5→32.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7968 0 117 331 8416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098270
X-RAY DIFFRACTIONf_angle_d1.08811213
X-RAY DIFFRACTIONf_dihedral_angle_d16.8663135
X-RAY DIFFRACTIONf_chiral_restr0.0721234
X-RAY DIFFRACTIONf_plane_restr0.0051432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4999-2.52830.2581290.2447251797
2.5283-2.55810.35381230.252657100
2.5581-2.58930.29661460.26032606100
2.5893-2.6220.32691350.25132650100
2.622-2.65650.321370.26142601100
2.6565-2.69290.29461370.25272654100
2.6929-2.73130.33241530.24092624100
2.7313-2.77210.33281340.25442607100
2.7721-2.81540.33591580.24022719100
2.8154-2.86150.28481220.24792567100
2.8615-2.91080.33791430.23042670100
2.9108-2.96370.29481290.22582632100
2.9637-3.02070.2951330.2262672100
3.0207-3.08230.26731530.22412606100
3.0823-3.14930.27081290.22272647100
3.1493-3.22250.28721600.2172587100
3.2225-3.3030.25971500.20762640100
3.303-3.39220.25181410.21152644100
3.3922-3.49190.24461510.2022599100
3.4919-3.60450.24331510.20582655100
3.6045-3.73310.26981300.20942608100
3.7331-3.88240.24061280.19032653100
3.8824-4.05880.2451240.1772669100
4.0588-4.27230.21691460.16332618100
4.2723-4.53940.21171290.17562652100
4.5394-4.88880.21261130.16662655100
4.8888-5.37890.22431410.18292640100
5.3789-6.15280.25751440.21832620100
6.1528-7.73510.22281470.21742628100
7.7351-32.84230.19951440.1944259598

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