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- PDB-2l6c: Solution structure of desulfothioredoxin from Desulfovibrio vulga... -

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Basic information

Entry
Database: PDB / ID: 2l6c
TitleSolution structure of desulfothioredoxin from Desulfovibrio vulgaris Hildenborough in its oxidized form
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / thioredoxin fold
Function / homology
Function and homology information


: / Glutaredoxin / Glutaredoxin domain profile. / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin, putative
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsGarcin, E.B. / Bornet, O. / Sebban-Kreuzer, C. / Guerlesquin, F.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural and mechanistic insights into unusual thiol disulfide oxidoreductase.
Authors: Garcin, E.B. / Bornet, O. / Elantak, L. / Vita, N. / Pieulle, L. / Guerlesquin, F. / Sebban-Kreuzer, C.
History
DepositionNov 18, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Feb 1, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,3841
Polymers12,3841
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Thioredoxin


Mass: 12384.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: Hildenborough / ATCC 29579 / NCIMB 8303 / Gene: DVU378, DVU_0378 / Plasmid: pJF / Production host: Escherichia coli (E. coli) / References: UniProt: Q72F37

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1513D CBCA(CO)NH
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D HBHA(CO)NH
11013D HN(CO)CA
11113D (H)CCH-TOCSY
11213D 1H-15N NOESY
11313D 1H-13C NOESY
11412D 1H-15N HSQC
11512D 1H-13C HSQC
11612D 1H-1H TOCSY
11712D 1H-1H NOESY
11813D CBCA(CO)NH
11913D HN(CA)CB
12013D HNCA
12113D HN(CO)CA
12213D HNCO
12313D HBHA(CO)NH
12413D (H)CCH-TOCSY
12513D 1H-15N NOESY
12613D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] oxidized desulfothioredoxin, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: oxidized desulfothioredoxin / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.1 / pH: 5.5 / Pressure: ambient / Temperature: 290 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
NameVersionDeveloperClassification
caraKeller and Wuthrichchemical shift assignment
Amber10Case, D.A. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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