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- PDB-1xfl: Solution Structure of Thioredoxin h1 from Arabidopsis Thaliana -

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Basic information

Entry
Database: PDB / ID: 1xfl
TitleSolution Structure of Thioredoxin h1 from Arabidopsis Thaliana
ComponentsThioredoxin h1
KeywordsELECTRON TRANSPORT / AT3G51030 / thioredoxin / structural genomics / protein structure initiative / CESG / PSI / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / glycerol ether metabolic process / positive regulation of catalytic activity / protein-disulfide reductase activity / enzyme activator 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 speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, CARTESIAN MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
AuthorsPeterson, F.C. / Lytle, B.L. / Sampath, S. / Vinarov, D. / Tyler, E. / Shahan, M. / Markley, J.L. / Volkman, B.F. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Protein Sci. / Year: 2005
Title: Solution structure of thioredoxin h1 from Arabidopsis thaliana.
Authors: Peterson, F.C. / Lytle, B.L. / Sampath, S. / Vinarov, D. / Tyler, E. / Shahan, M. / Markley, J.L. / Volkman, B.F.
History
DepositionSep 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin h1


Theoretical massNumber of molelcules
Total (without water)13,9471
Polymers13,9471
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 #1closest to the average

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Components

#1: Protein Thioredoxin h1 / TRXh1 / TRX-H-1 / Thioredoxin H-Type 1


Mass: 13947.103 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: WHEAT GERM CELL-FREE, IN VITRO EXPRESSION / Gene: At3g51030 / Plasmid: pEU(N)His6-at3G51030 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: P29448

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1213D 13C-SEPARATED NOESY
1313D 13C- SEPARATED NOESY-AROMATIC
NMR detailsText: CHEMICAL SHIFT ASSIGNMENTS WERE OBTAINED FROM STANDARD 3D TRIPLE-RESONANCE EXPERIMENTS, USING THE AUTOMATED METHOD OF GARANT (CHRISTIAN BARTELS).

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Sample preparation

DetailsContents: 0.5 MM U-15N,13C At3G51030;10MM PHOSPHATE BUFFER; 50MM KCL; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM KCL / pH: 5.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA 1.0.6, XPLOR-NIH2.0.6GUENTERT (CYANA), CLORE (XPLOR-NIH)refinement
XwinNMR3.1collection
NMRPipe2.1processing
XEASY1.3.1data analysis
SPSCAN1.1.0data analysis
RefinementMethod: TORSION ANGLE DYNAMICS, CARTESIAN MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Software ordinal: 1
Details: INITIAL STRUCTURES WERE GENERATED USING THE CANDID MODULE OF CYANA. ADDITIONAL NOE ASSIGNMENTS WERE DETERMINED MANUALLY. PHI AND PSI TORSION ANGLE CONSTRAINTS WERE GENERATED FROM CHEMICAL ...Details: INITIAL STRUCTURES WERE GENERATED USING THE CANDID MODULE OF CYANA. ADDITIONAL NOE ASSIGNMENTS WERE DETERMINED MANUALLY. PHI AND PSI TORSION ANGLE CONSTRAINTS WERE GENERATED FROM CHEMICAL SHIFT DATABASE SEARCHING USING THE PROGRAM TALOS (G. CORNILESCU).
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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