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- PDB-8qpd: Structure of thioredoxin m from pea -

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Basic information

Entry
Database: PDB / ID: 8qpd
TitleStructure of thioredoxin m from pea
ComponentsThioredoxin M-type, chloroplastic
KeywordsPLANT PROTEIN / STRUCTURE FROM CYANA 2.1 / redox process
Function / homology
Function and homology information


protein-disulfide reductase activity / chloroplast / enzyme activator activity
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Thioredoxin M-type, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNeira, J.L. / Camara Artigas, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Generalitat ValencianaCAICO/2021/0135 Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Three-dimensional solution structure, dynamics and binding of thioredoxin m from Pisum sativum.
Authors: Neira, J.L. / Palomino-Schatzlein, M. / Rejas, V. / Traverso, J.A. / Rico, M. / Lopez-Gorge, J. / Chueca, A. / Camara-Artigas, A.
History
DepositionOct 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin M-type, chloroplastic


Theoretical massNumber of molelcules
Total (without water)11,9931
Polymers11,9931
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300target function
RepresentativeModel #1target function

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Components

#1: Protein Thioredoxin M-type, chloroplastic


Mass: 11992.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P48384

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
232isotropic13D HN(CA)CB
242isotropic13D HNCO
252isotropic13D HNCA
262isotropic13D HBHA(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12.0 mM Thioredoxin m from pea sativum, 90% H2O/10% D2O1H_sample90% H2O/10% D2O
solution22.0 mM [U-100% 13C; U-100% 15N; U-80% 2H] Thioredoxin m from pea sativum, 90% H2O/10% D2O13C,15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMThioredoxin m from pea sativumnatural abundance1
2.0 mMThioredoxin m from pea sativum[U-100% 13C; U-100% 15N; U-80% 2H]2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10.050 mM1H_sample5.91 atm303 K
20.050 mM13C,15N_sample5.91 atm303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 300 / Conformers submitted total number: 20

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