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- PDB-2myg: Solution structure of the dithiolic glutaredoxin 2-C-Grx1 from th... -

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Basic information

Entry
Database: PDB / ID: 2myg
TitleSolution structure of the dithiolic glutaredoxin 2-C-Grx1 from the pathogen Trypanosoma brucei brucei
ComponentsDithiol glutaredoxin 1
KeywordsOXIDOREDUCTASE / glutaredoxin / trypanothione / Trypanosomes / ELECTRON TRANSPORT
Function / homology
Function and homology information


protein-disulfide reductase activity / electron transfer activity
Similarity search - Function
Glutaredoxin subgroup / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutaredoxin, putative / Dithiol glutaredoxin 1
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsSturlese, M. / Stefani, M. / Manta, B. / Mammi, S. / Comini, M. / Bellanda, M.
CitationJournal: To be Published
Title: Solution structure of the dithiolic glutaredoxin 2-C-Grx1 from the pathogen Trypanosoma brucei brucei
Authors: Sturlese, M. / Lelli, M. / Manta, B. / Mammi, S. / Comini, M.A. / Bellanda, M.
History
DepositionJan 22, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dithiol glutaredoxin 1


Theoretical massNumber of molelcules
Total (without water)10,7181
Polymers10,7181
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 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Dithiol glutaredoxin 1


Mass: 10718.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / Gene: grx1, TbgDal_XI1450 / Production host: Escherichia coli (E. coli) / References: UniProt: E7AIJ0, UniProt: D0A5S8*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D HNCO
1313DHN(CA)CO
1413D CBCA(CO)NH
1513D HBHA(CO)NH
1613D (H)CCH-TOCSY
1713D H(CCO)NH
1813D H(CCO)NH
1912D (H)CB(CGCC)H-TOCSY (PHE-OPTIMIZED)
11012D (H)CB(CGCC)H-TOCSY (TYR-OPTIMIZED)
11112D (H)CB(CGCC)H-TOCSY (HIS-OPTIMIZED)
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic
11413D 1H-15N NOESY

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Sample preparation

DetailsContents: 50 mM sodium phosphate-1, 150 mM sodium chloride-2, 10 mM DTT-3, 1 mM EDTA-4, 0.05 % sodium azide-5, 0.2 mM PMSF-6, 1 mM [U-13C; U-15N] Tb 2-C-Grx1-7, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
150 mMsodium chloride-21
10 mMDTT-31
1 mMEDTA-41
0.05 %sodium azide-51
0.2 mMPMSF-61
1 mMTb 2-C-Grx1-7[U-13C; U-15N]1
Sample conditionspH: 7.2 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
CARAKeller and Wuthrichchemical shift assignment
UNIO'10Torsten Herrmannpeak picking
UNIO'10Torsten Herrmannnoesy assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: restrained Molecular Dynamics using AMPS-NMR server
NMR constraintsNOE constraints total: 1649 / NOE intraresidue total count: 401 / NOE long range total count: 372 / NOE medium range total count: 331 / NOE sequential total count: 399
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0 Å

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