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- PDB-3wyw: Structural characterization of catalytic site of a Nilaparvata lu... -

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Basic information

Entry
Database: PDB / ID: 3wyw
TitleStructural characterization of catalytic site of a Nilaparvata lugens delta-class glutathione transferase
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / glutathione conjugation / glutathione
Function / homology
Function and homology information


transferase activity
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / 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 ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / 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
GLUTATHIONE / Glutathione S-transferase
Similarity search - Component
Biological speciesNilaparvata lugens (brown planthopper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYamamoto, K. / Higashiura, A. / Nakagawa, A.
CitationJournal: Arch.Biochem.Biophys. / Year: 2014
Title: Structural characterization of the catalytic site of a Nilaparvata lugens delta-class glutathione transferase.
Authors: Yamamoto, K. / Higashiura, A. / Hossain, M.T. / Yamada, N. / Shiotsuki, T. / Nakagawa, A.
History
DepositionSep 9, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: 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

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Assembly

Deposited unit
A: Glutathione S-transferase
B: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6218
Polymers47,7582
Non-polymers8636
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-21 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.552, 49.104, 74.184
Angle α, β, γ (deg.)90.00, 99.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutathione S-transferase / Glutathione s-transferase D2


Mass: 23879.201 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nilaparvata lugens (brown planthopper) / References: UniProt: Q8N0B3
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1M LiCl2, 30% PEG 6000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorDetector: CCD / Date: Nov 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→36.54 Å / Num. obs: 42310 / % possible obs: 21.19 % / Observed criterion σ(F): 27.3 / Observed criterion σ(I): 3.78
Reflection shellResolution: 1.7→1.73 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MERLOTphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.5 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.508 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21715 2125 5 %RANDOM
Rwork0.17456 ---
obs0.17676 40131 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.322 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.07 Å2
2---0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 56 338 3722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.023539
X-RAY DIFFRACTIONr_bond_other_d0.0010.023379
X-RAY DIFFRACTIONr_angle_refined_deg1.722.0024794
X-RAY DIFFRACTIONr_angle_other_deg2.27937832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0145445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.4125.455154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3715598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.547158
X-RAY DIFFRACTIONr_chiral_restr0.1140.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214028
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02770
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_it2.4922.0971726
X-RAY DIFFRACTIONr_mcbond_other2.4882.0951725
X-RAY DIFFRACTIONr_mcangle_it3.2663.1272159
X-RAY DIFFRACTIONr_mcangle_other3.2663.1292160
X-RAY DIFFRACTIONr_scbond_it3.5392.391813
X-RAY DIFFRACTIONr_scbond_other3.5372.3891813
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9913.4342626
X-RAY DIFFRACTIONr_long_range_B_refined5.76818.0884428
X-RAY DIFFRACTIONr_long_range_B_other5.67617.6374282
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 132 -
Rwork0.221 2978 -
obs--98.64 %

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