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- PDB-5d9w: Dehydroascorbate reductase (OsDHAR) complexed with ASA -

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Basic information

Entry
Database: PDB / ID: 5d9w
TitleDehydroascorbate reductase (OsDHAR) complexed with ASA
ComponentsDehydroascorbate reductaseGlutathione dehydrogenase (ascorbate)
KeywordsPLANT PROTEIN / OsDHAR / Oryza sativa L. japonica / ascorbate
Function / homology
Function and homology information


ascorbate glutathione cycle / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / cellular oxidant detoxification / glutathione transferase / glutathione transferase activity / cytosol
Similarity search - Function
Dehydroascorbate reductases DHAR1/2/3/4 / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-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 / 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 ...Dehydroascorbate reductases DHAR1/2/3/4 / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-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 / 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
ASCORBIC ACID / Probable glutathione S-transferase DHAR1, cytosolic
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6897 Å
AuthorsDo, H. / Lee, J.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Korea Polar Research InstitutePE15070 Korea, Republic Of
Rural Development AdministrationPJ011122 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2016
Title: Structural understanding of the recycling of oxidized ascorbate by dehydroascorbate reductase (OsDHAR) from Oryza sativa L. japonica
Authors: Do, H. / Kim, I.S. / Jeon, B.W. / Lee, C.W. / Park, A.K. / Wi, A.R. / Shin, S.C. / Park, H. / Kim, Y.S. / Yoon, H.S. / Kim, H.W. / Lee, J.H.
History
DepositionAug 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_oper_list ...chem_comp / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Dehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8012
Polymers25,6251
Non-polymers1761
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint2 kcal/mol
Surface area10390 Å2
Unit cell
Length a, b, c (Å)46.848, 47.279, 50.992
Angle α, β, γ (deg.)90.00, 108.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dehydroascorbate reductase / Glutathione dehydrogenase (ascorbate) / Os05g0116100 protein / cDNA clone:001-040-D08 / full insert sequence / cDNA clone:J023074C02


Mass: 25625.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: P0496H07.8, Os05g0116100, OJ1654_B10.18 / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3) / References: UniProt: Q65XA0
#2: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Comment: medication*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 41.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100mM Bis-Tris HCl, pH 6.6, 28%(w/v) PEG3350, 10mM CaCl2
PH range: 6.1-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6897→30 Å / Num. obs: 23333 / % possible obs: 98.2 % / Redundancy: 7.4 % / Net I/σ(I): 53.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6897→28.611 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 1097 4.7 %
Rwork0.2029 --
obs0.2045 23319 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6897→28.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 12 37 1700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061708
X-RAY DIFFRACTIONf_angle_d0.9082323
X-RAY DIFFRACTIONf_dihedral_angle_d12.323626
X-RAY DIFFRACTIONf_chiral_restr0.036259
X-RAY DIFFRACTIONf_plane_restr0.004296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6897-1.76660.31541190.27542596X-RAY DIFFRACTION93
1.7666-1.85970.28261440.25162758X-RAY DIFFRACTION98
1.8597-1.97620.29421270.24242795X-RAY DIFFRACTION98
1.9762-2.12870.25171380.21992796X-RAY DIFFRACTION98
2.1287-2.34290.27271670.22872773X-RAY DIFFRACTION99
2.3429-2.68170.26761370.23652810X-RAY DIFFRACTION99
2.6817-3.37770.27671470.22332846X-RAY DIFFRACTION99
3.3777-28.61520.17041180.15992848X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 10.1829 Å / Origin y: -0.5841 Å / Origin z: 8.8692 Å
111213212223313233
T0.2439 Å20.0229 Å2-0.0491 Å2-0.1886 Å20.024 Å2--0.2233 Å2
L2.7579 °2-0.772 °20.0067 °2-3.7175 °2-0.5514 °2--2.0195 °2
S-0.2201 Å °-0.3159 Å °0.0913 Å °0.4994 Å °0.1267 Å °-0.4033 Å °-0.121 Å °-0.025 Å °0.0722 Å °
Refinement TLS groupSelection details: all

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