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- PDB-6ap5: H, 13C, and 15N Chemical Shift Assignments and structure of Thior... -

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Basic information

Entry
Database: PDB / ID: 6ap5
TitleH, 13C, and 15N Chemical Shift Assignments and structure of Thioredoxin from Mycobacterium thermoresistibile ATCC 19527 and NCTC 10409
ComponentsThioredoxin
KeywordsSTRUCTURAL PROTEIN / STRUCTURE FROM CYANA 3.97 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


glycerol ether metabolic process / 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
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTang, C.T. / Yang, F.Y. / Varani, G.V. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: H, 13C, and 15N Chemical Shift Assignments and structure of Thioredoxin from Mycobacterium thermoresistibile ATCC 19527 and NCTC 10409
Authors: Tang, C.T. / Yang, F.Y. / Varani, G.V.
History
DepositionAug 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 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_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,5081
Polymers12,5081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Thioredoxin


Mass: 12508.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316) (bacteria)
Strain: ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316
Gene: KEK_10718 / Production host: Escherichia coli (E. coli) / References: UniProt: G7CIN2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HNCA
151isotropic13D HBHA(CO)NH
162isotropic13D (H)CCH-TOCSY
171isotropic13D H(CCO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-95% 13C; U-95% 15N] Thioredoxin, 100 mM sodium chloride, 25 mM sodium phosphate, 2 mM DTT, 10 % v/v D20, 90% H2O/10% D2O15N13C_sample90% H2O/10% D2O
solution21 mM [U-95% 13C; U-95% 15N] Thioredoxin, 100 mM sodium chloride, 25 mM sodium phosphate, 2 mM DTT, 100 % v/v D2O, 100% D2O13C15N_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMThioredoxin[U-95% 13C; U-95% 15N]1
100 mMsodium chloridenatural abundance1
25 mMsodium phosphatenatural abundance1
2 mMDTTnatural abundance1
10 % v/vD20natural abundance1
1 mMThioredoxin[U-95% 13C; U-95% 15N]2
100 mMsodium chloridenatural abundance2
25 mMsodium phosphatenatural abundance2
2 mMDTTnatural abundance2
100 % v/vD2Onatural abundance2
Sample conditionsIonic strength: 100 mM / Label: condition_1 / pH: 6.0 / Pressure: 1 Pa / 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
AnalysisCCPNrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AnalysisCCPNchemical shift assignment
AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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