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- PDB-1nho: Structural and Functional characterization of a Thioredoxin-like ... -

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Basic information

Entry
Database: PDB / ID: 1nho
TitleStructural and Functional characterization of a Thioredoxin-like Protein from Methanobacterium thermoautotrophicum
ComponentsProbable Thioredoxin
KeywordsOXIDOREDUCTASE / beta sheet / alpha helix
Function / homology
Function and homology information


protein-disulfide reductase activity / cell redox homeostasis / electron transfer activity / cytoplasm
Similarity search - Function
Thioredoxins/glutaredoxin / Thioredoxin domain / Glutaredoxin active site / Glutaredoxin active site. / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Thioredoxins/glutaredoxin / Thioredoxin domain / Glutaredoxin active site / Glutaredoxin active site. / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable Thioredoxin
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsAmegbey, G.Y. / Monzavi, H. / Habibi-Nazhad, B. / Bhattacharyya, S. / Wishart, D.S.
CitationJournal: Biochemistry / Year: 2003
Title: Structural and Functional Characterization of a Thioredoxin-like Protein (Mt0807) from Methanobacterium thermoautotrophicum
Authors: Amegbey, G.Y. / Monzavi, H. / Habibi-Nazhad, B. / Bhattacharyya, S. / Wishart, D.S.
History
DepositionDec 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 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: Probable Thioredoxin


Theoretical massNumber of molelcules
Total (without water)9,4891
Polymers9,4891
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 / 20structures with acceptable covalent geometry
RepresentativeModel #8lowest energy and secondary structure representing those of chemical shift

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Components

#1: Protein Probable Thioredoxin / Glutaredoxin-like protein


Mass: 9488.942 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H / Gene: MTH807 / Plasmid: pET15b (Novagen) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O26898

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY and HSQC
1313D TOCSY HSQC
1413D NOESY HSQC
1513D HN(CA)CB
1613D HNCO
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Mt0807 U-15N, U-13C 50mM phosphate buffer, 100mM NaCL 1mM DSS, 0.06% NaN3, pH 6.0, 90% H2O, 10% D2O90% H2O/10% D2O
21mM Mt0807 U-15N, 50mM phosphate buffer, 100mM NaCL 1mM DSS, 0.06% NaN3, pH 6.0, 90% H2O, 10% D2O90% H2O/10% D2O
31mM Mt0807, 50mM phosphate buffer, 100mM NaCL 1mM DSS, 0.06% NaN3, pH 6.0, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM NaH2PO4, 100mM NaCL 6ambient 298 K
250mM NaH2PO4, 100mM NaCL 6ambient 298 K
350mM NaH2PO4, 100mM NaCL 6ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVarian Inc.collection
VNMR6.1C + PROC3D extensionMonzavi, H.processing
X-PLOR (random.inp, dgsa.inp)3.851Nilges, M., Gronenborn, A.M., Brunger, A.T., Clore, G.M., Kuszewski, J.structure solution
X-PLOR3.851Nilges, M., Gronenborn, A.M., Brunger, A.T., Clore, G.M., Kuszewski, J., Garrett, Hancock, Lodi, Vuister, Qinrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 997 restraints, 873 are NOE-derived distance constraints, 82 dihedral angle restraints, 42 distance restraints from hydrogen bonds. The structure was ...Details: The structures are based on a total of 997 restraints, 873 are NOE-derived distance constraints, 82 dihedral angle restraints, 42 distance restraints from hydrogen bonds. The structure was refined using refine.inp and Mini_shift_coup.inp.
NMR representativeSelection criteria: lowest energy and secondary structure representing those of chemical shift
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 20 / Conformers submitted total number: 20

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