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- PDB-5mye: Solution structure of C20S variant of Dehydroascorbate reductase ... -

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Basic information

Entry
Database: PDB / ID: 5mye
TitleSolution structure of C20S variant of Dehydroascorbate reductase 3A from Populus trichocarpa in complex with dehydroascorbic acid.
ComponentsDehydroascorbate reductase family protein
KeywordsOXIDOREDUCTASE / Glutathione transferase Dehydroascorbate reductase Plant
Function / homology
Function and homology information


ascorbate glutathione cycle / glutathione dehydrogenase (ascorbate) activity / glutathione dehydrogenase (ascorbate) / glutathione transferase activity
Similarity search - Function
Dehydroascorbate reductases DHAR1/2/3/4 / 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 ...Dehydroascorbate reductases DHAR1/2/3/4 / 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
Chem-UU3 / glutathione dehydrogenase (ascorbate)
Similarity search - Component
Biological speciesPopulus trichocarpa (black cottonwood)
MethodSOLUTION NMR / molecular dynamics
AuthorsRoret, T. / Tsan, P.
CitationJournal: Biochem. J. / Year: 2016
Title: Insights into ascorbate regeneration in plants: investigating the redox and structural properties of dehydroascorbate reductases from Populus trichocarpa.
Authors: Lallement, P.A. / Roret, T. / Tsan, P. / Gualberto, J.M. / Girardet, J.M. / Didierjean, C. / Rouhier, N. / Hecker, A.
History
DepositionJan 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Oct 30, 2019Group: Data collection / Database references / Category: pdbx_database_related / pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dehydroascorbate reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5222
Polymers24,3481
Non-polymers1741
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9540 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1target function

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Components

#1: Protein Dehydroascorbate reductase family protein / dehydroascorbate reductase 3A


Mass: 24348.131 Da / Num. of mol.: 1 / Mutation: C20S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Gene: POPTR_0008s04920g / Production host: Escherichia coli (E. coli) / References: UniProt: B9HM36
#2: Chemical ChemComp-UU3 / (5R)-5-[(1S)-1,2-bis(oxidanyl)ethyl]oxolane-2,3,4-trione / Dehydroascorbic Acid / DHA


Mass: 174.108 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 2D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.37 mM [U-100% 15N] dehydroascorbate reductase 3A, 90% H2O/10% D2O15N90% H2O/10% D2O
solution20.37 mM [U-100% 15N] dehydroascorbate reductase 3A, 47 mM Dehydroascorbic acid, 90% H2O/10% D2O15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.37 mMdehydroascorbate reductase 3A[U-100% 15N]1
0.37 mMdehydroascorbate reductase 3A[U-100% 15N]2
47 mMDehydroascorbic acidnatural abundance2
Sample conditionsIonic strength: 50 mM / Label: condition_1 / pH: 8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
YASARAYASARArefinement
UCSF ChimeraUCSF Chimerarefinement
PELE web serverPELEstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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