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- PDB-5vo7: NMR Assignment and Structure of Thioredoxin (Rv1471 ortholog) fro... -

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Basic information

Entry
Database: PDB / ID: 5vo7
TitleNMR Assignment and Structure of Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)155
ComponentsThioredoxin
KeywordsELECTRON TRANSPORT / PROTEIN NMR Thioredoxin Mycobacterium smegmatis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / PROTEIN
Function / homology
Function and homology information


: / protein-disulfide reductase activity / cell redox homeostasis
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin / Thioredoxin
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBarnwal, R.P. / Varani, G. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Assignment and Structure of Thioredoxin (Rv1471 ortholog) type protein from Mycobacterium smegmatis ATCC 700084 / mc(2)155
Authors: Barnwal, R.P. / Varani, G.
History
DepositionMay 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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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)11,6341
Polymers11,6341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1target function

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Components

#1: Protein Thioredoxin


Mass: 11634.341 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: trxA_2, ERS451418_06713 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6J3B8, UniProt: O30974*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic23D CBCA(CO)NH
141isotropic23D HN(CA)CB
151isotropic23D HNCO
191isotropic23D (H)CCH-TOCSY
181isotropic23D HBHA(CO)NH
171isotropic13D 1H-15N NOESY
161isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 1.1 mM [U-99% 13C; U-99% 15N] Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C, 93% H2O/7% D2O
Label: 13C 15N / Solvent system: 93% H2O/7% D2O
SampleConc.: 1.1 mM
Component: Thioredoxin (Rv1471 ortholog) from Mycobacterium smegmatis ATCC 700084 / mc(2)15513C
Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 100 mM / Label: Conditions_1 / pH: 6 / Pressure: AMBIENT atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIBrukerAVANCE II6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichrefinement
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
AnalysisCCPNchemical shift assignment
TopSpinBruker Biospincollection
CcpNMRCCPNpeak picking
CcpNMRCCPNdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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