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- PDB-1quw: SOLUTION STRUCTURE OF THE THIOREDOXIN FROM BACILLUS ACIDOCALDARIUS -

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Basic information

Entry
Database: PDB / ID: 1quw
TitleSOLUTION STRUCTURE OF THE THIOREDOXIN FROM BACILLUS ACIDOCALDARIUS
ComponentsTHIOREDOXIN
KeywordsELECTRON TRANSPORT / ALPHA/BETA OPEN-TWISTED PROTEIN / THIOL-DISULFIDE
Function / homology
Function and homology information


protein-disulfide reductase activity / cell redox homeostasis / cytosol
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 speciesAlicyclobacillus acidocaldarius (bacteria)
MethodSOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS, RESTRAINED ENERGY MINIMISATION
AuthorsNicastro, G. / de Chiara, C. / Pedone, E. / Tato, M. / Rossi, M.
Citation
Journal: Eur.J.Biochem. / Year: 2000
Title: NMR solution structure of a novel thioredoxin from Bacillus acidocaldarius possible determinants of protein stability.
Authors: Nicastro, G. / De Chiara, C. / Pedone, E. / Tato, M. / Rossi, M. / Bartolucci, S.
#1: Journal: Biochem.J. / Year: 1997
Title: Thioredoxin from Bacillus Acidocaldarius: Characterization, High-Level Expression in E. Coli and Molecular Modeling
Authors: Bartolucci, S. / Guagliardi, A. / Pedone, E. / De Pascale, D. / Cannio, R. / Camardella, L. / Rossi, M. / Nicastro, G. / de Chiara, C. / Facci, P. / Mascetti, G. / Nicolini, C.
#2: Journal: J.Biomol.Struct.Dyn. / Year: 1998
Title: Computational Analysis of the Thermal Stability in Thioredoxins: a Molecular Dynamics Approach
Authors: Pedone, E.M. / Bartolucci, S. / Rossi, M. / Saviano, M.
#3: Journal: Biochem.J. / Year: 1999
Title: Prediction and Experimental Testing of the Bacillus acidocaldarius Thioredoxin Stability
Authors: Pedone, E. / Cannio, R. / Saviano, M. / Rossi, M. / Bartolucci, S.
History
DepositionJul 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)11,5851
Polymers11,5851
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 / 50STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS
Representative

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Components

#1: Protein THIOREDOXIN


Mass: 11585.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius (bacteria)
Description: BACTERIUM / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / References: UniProt: P80579
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D NOESY
131TOCSY
241DQF-COSY
2512D NOESY
261TOCSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D AND 3D HOMONUCLEAR TECHNIQUES.

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Sample preparation

DetailsContents: 1.2MM RECOMBINANT THIOREDOXIN FROM BACILLUS ACIDOCALDARIUS; 50MM PHOSPHATE BUFFER NA; 90% H2O, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM BUFFER PHOSPHATE 5.8AMBIENT 300 K
250mM BUFFER PHOSPHATE 5.8AMBIENT 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR4.1VARIANcollection
FelixFELIX95HARE, D.data analysis
Discover95BIOSYMstructure solution
Discover95BIOSYMrefinement
RefinementMethod: SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS, RESTRAINED ENERGY MINIMISATION
Software ordinal: 1
Details: THE STRUCTURE ARE BASED ON A TOTAL OF 2276 NOE-DERIVED DISTANCE CONSTRAINTS, 99 DIHEDRAL ANGLE RESTRAINTS.
NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS
Conformers calculated total number: 50 / Conformers submitted total number: 20

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