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- PDB-5d9x: Dehydroascorbate reductase complexed with GSH -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5d9x
TitleDehydroascorbate reductase complexed with GSH
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
GLUTATHIONE / Probable glutathione S-transferase DHAR1, cytosolic
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)25,9733
Polymers25,6251
Non-polymers3472
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-12 kcal/mol
Surface area10690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.890, 47.600, 51.790
Angle α, β, γ (deg.)90.00, 107.00, 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 / Mutation: C20S
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: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.36 Å3/Da / Density % sol: 42.97 %
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: 1.68→49.53 Å / Num. obs: 24925 / % possible obs: 98.9 % / Redundancy: 7 % / Net I/σ(I): 16.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→39.476 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 1283 5.15 %
Rwork0.1916 --
obs0.1934 24909 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→39.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 21 85 1757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091715
X-RAY DIFFRACTIONf_angle_d1.2352330
X-RAY DIFFRACTIONf_dihedral_angle_d12.754628
X-RAY DIFFRACTIONf_chiral_restr0.056259
X-RAY DIFFRACTIONf_plane_restr0.005299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.679-1.74620.25911590.20852560X-RAY DIFFRACTION99
1.7462-1.82570.25641310.19992620X-RAY DIFFRACTION100
1.8257-1.9220.23921340.20782657X-RAY DIFFRACTION100
1.922-2.04240.29371270.20222646X-RAY DIFFRACTION100
2.0424-2.20010.2321270.1892633X-RAY DIFFRACTION100
2.2001-2.42140.20931490.20012639X-RAY DIFFRACTION100
2.4214-2.77180.22691600.20682636X-RAY DIFFRACTION100
2.7718-3.49180.23441470.20262662X-RAY DIFFRACTION100
3.4918-39.48680.20241490.1662573X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 10.353 Å / Origin y: -0.4702 Å / Origin z: 8.9774 Å
111213212223313233
T0.1539 Å20.0128 Å2-0.0166 Å2-0.1371 Å20.0321 Å2--0.1257 Å2
L1.6351 °2-0.3455 °2-0.224 °2-2.9131 °2-0.329 °2--1.6719 °2
S-0.1307 Å °-0.1972 Å °-0.0788 Å °0.396 Å °0.0602 Å °-0.1348 Å °-0.0618 Å °0.0248 Å °0.0462 Å °
Refinement TLS groupSelection details: all

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