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- PDB-2mmn: Solution Structure of the Reduced Thioredoxin from Plasmodium fal... -

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Basic information

Entry
Database: PDB / ID: 2mmn
TitleSolution Structure of the Reduced Thioredoxin from Plasmodium falciparum
ComponentsThioredoxin
KeywordsELECTRON TRANSPORT / Plasmodium falciparum / Thioredoxin
Function / homology
Function and homology information


protein-disulfide reductase activity / 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 speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsMunte, C. / Kalbitzer, H. / Schirmer, R.
CitationJournal: To be Published
Title: Solution Structure of Plasmodium falciparum Thioredoxin
Authors: Munte, C. / Kalbitzer, H. / Schirmer, R.
History
DepositionMar 16, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)11,6991
Polymers11,6991
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Thioredoxin / / Trx


Mass: 11699.276 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF14_0545 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7KQL8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1232D 1H-13C HSQC
1323D HNCA
1423D HNCO
1533D (H)CCH-TOCSY
1612D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM protein-1, 10 mM potassium chloride-2, 1 mM sodium azide-3, 0.1 mM DSS-4, 1 mM DTT-5, 93% H2O/7% D2O93% H2O/7% D2O
21 mM [U-100% 13C; U-100% 15N] protein-6, 10 mM potassium chloride-7, 1 mM sodium azide-8, 0.1 mM DSS-9, 1 mM DTT-10, 93% H2O/7% D2O93% H2O/7% D2O
31 mM [U-100% 13C; U-100% 15N] protein-11, 10 mM potassium chloride-12, 1 mM sodium azide-13, 0.1 mM DSS-14, 1 mM DTT-15, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein-11
10 mMpotassium chloride-21
1 mMsodium azide-31
0.1 mMDSS-41
1 mMDTT-51
1 mMprotein-6[U-100% 13C; U-100% 15N]2
10 mMpotassium chloride-72
1 mMsodium azide-82
0.1 mMDSS-92
1 mMDTT-102
1 mMprotein-11[U-100% 13C; U-100% 15N]3
10 mMpotassium chloride-123
1 mMsodium azide-133
0.1 mMDSS-143
1 mMDTT-153
Sample conditionspH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
AUREMOLBruker Biospindata analysis
AUREMOLBruker Biospinpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10 / Representative conformer: 1

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