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- PDB-5lol: Glutathione-bound Dehydroascorbate Reductase 2 of Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 5lol
TitleGlutathione-bound Dehydroascorbate Reductase 2 of Arabidopsis thaliana
ComponentsGlutathione S-transferase DHAR2
KeywordsTRANSFERASE / Dehydroascorbate Reductase / Glutathione Dehydrogenase
Function / homology
Function and homology information


protein glutathionylation / acquisition of seed longevity / positive regulation of salicylic acid mediated signaling pathway / ascorbate glutathione cycle / glutathione dehydrogenase (ascorbate) activity / L-ascorbic acid metabolic process / glutathione dehydrogenase (ascorbate) / glutathione binding / glutathione transferase / glutathione transferase activity ...protein glutathionylation / acquisition of seed longevity / positive regulation of salicylic acid mediated signaling pathway / ascorbate glutathione cycle / glutathione dehydrogenase (ascorbate) activity / L-ascorbic acid metabolic process / glutathione dehydrogenase (ascorbate) / glutathione binding / glutathione transferase / glutathione transferase activity / mitochondrion / plasma membrane / cytosol
Similarity search - Function
Dehydroascorbate reductases DHAR1/2/3/4 / Glutathione S-transferase, N-terminal domain / 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. ...Dehydroascorbate reductases DHAR1/2/3/4 / Glutathione S-transferase, N-terminal domain / 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 / Glutathione S-transferase DHAR2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsYoung, D.R. / Pallo, A. / Bodra, N. / Messens, J.
Funding support Belgium, India, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G.0305.12, and G0D7914N Belgium
Flanders Hercules FoundationHERC16 and UABR/09/005 Belgium
IIndian Council of Agricultural Research (ICAR) India
CitationJournal: Sci Rep / Year: 2017
Title: Arabidopsis thaliana dehydroascorbate reductase 2: Conformational flexibility during catalysis.
Authors: Bodra, N. / Young, D. / Astolfi Rosado, L. / Pallo, A. / Wahni, K. / De Proft, F. / Huang, J. / Van Breusegem, F. / Messens, J.
History
DepositionAug 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase DHAR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0884
Polymers23,5921
Non-polymers4953
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-13 kcal/mol
Surface area10880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.107, 67.002, 68.026
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

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Components

#1: Protein Glutathione S-transferase DHAR2 / Chloride intracellular channel homolog 2 / CLIC homolog 2 / Glutathione-dependent dehydroascorbate ...Chloride intracellular channel homolog 2 / CLIC homolog 2 / Glutathione-dependent dehydroascorbate reductase 2 / GSH-dependent dehydroascorbate reductase 2


Mass: 23592.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal residues 1 & 2 (G & P) belong to the protease cleavage site
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cell: Cytoplasm / Gene: DHAR2, DHAR, At1g75270, F22H5.1 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9FRL8, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 20 mg/ml protein (in 20 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA) was mixed with 2 M ammonium sulfate, 0.1 M sodium acetate at a 1:1 ratio

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.2→47.11 Å / Num. obs: 10362 / % possible obs: 90.4 % / Redundancy: 5.9 % / Biso Wilson estimate: 32.484 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Net I/σ(I): 13 / Num. measured all: 60869 / Scaling rejects: 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.2-2.271.40.7510.429146
9.07-47.115.80.0450.999199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.2 Å38.73 Å
Translation2.2 Å38.73 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1refinement
Aimless0.5.23data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5d9t

5d9t


Resolution: 2.3→38.73 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.222 --Random selection
Rwork0.2118 ---
obs-2736 87.1 %-
Displacement parametersBiso max: 85.18 Å2 / Biso mean: 36.0509 Å2 / Biso min: 19.19 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 31 50 1692
LS refinement shellHighest resolution: 2.3 Å / Rfactor Rfree: 0.2857 / Rfactor Rwork: 0.268

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