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- PDB-2mxn: NMR Structure of the mature form of Trypanosoma brucei 1CGrx1 -

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Basic information

Entry
Database: PDB / ID: 2mxn
TitleNMR Structure of the mature form of Trypanosoma brucei 1CGrx1
ComponentsMono-cysteine glutaredoxin
KeywordsPROTEIN BINDING / 1CGRX1 / Monothiol Glutaredoxin / Iron-Sulfur cluster / Trypanosomes / Trypanothione / ISC-BINDING PROTEIN
Function / homology
Function and homology information


iron-sulfur cluster binding / metal ion binding
Similarity search - Function
Monothiol glutaredoxin-related / Glutaredoxin, PICOT-like / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Thioredoxin-like superfamily
Similarity search - Domain/homology
Glutaredoxin-like protein, putative / Mono-cysteine glutaredoxin
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsSturlese, M. / Bertarello, A. / Manta, B. / Lelli, M. / Mammi, S. / Comini, M. / Bellanda, M.
CitationJournal: Sci Rep / Year: 2018
Title: The lineage-specific, intrinsically disordered N-terminal extension of monothiol glutaredoxin 1 from trypanosomes contains a regulatory region.
Authors: Sturlese, M. / Manta, B. / Bertarello, A. / Bonilla, M. / Lelli, M. / Zambelli, B. / Grunberg, K. / Mammi, S. / Comini, M.A. / Bellanda, M.
History
DepositionJan 8, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Structure summary
Revision 1.2Apr 11, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct / struct_keywords / struct_ref_seq_dif
Item: _entity.pdbx_fragment / _entity_src_gen.gene_src_strain ..._entity.pdbx_fragment / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _struct.title / _struct_keywords.text / _struct_ref_seq_dif.details
Revision 1.3Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4May 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mono-cysteine glutaredoxin


Theoretical massNumber of molelcules
Total (without water)16,0821
Polymers16,0821
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Mono-cysteine glutaredoxin


Mass: 16082.497 Da / Num. of mol.: 1 / Fragment: unp residues 43-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: mgrx / Production host: Escherichia coli (E. coli) / References: UniProt: Q2UZM9, UniProt: C9ZXG5*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY aliphatic
1312D 1H-13C HSQC aromatic

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Sample preparation

DetailsContents: 1.5 mM [U-13C; U-15N] protein, 150 mM sodium chloride, 10 mM DTT, 0.05 % sodium azide, 0.2 mM PMSF, 1 mM EDTA, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMentity-1[U-13C; U-15N]1
150 mMsodium chloride-21
10 mMDTT-31
0.05 %sodium azide-41
0.2 mMPMSF-51
1 mMEDTA-61
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE10001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CARAKeller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
UNIO'102.02(UNIO)Torsten Herrmannstructure solution
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1237 / NOE intraresidue total count: 276 / NOE long range total count: 264 / NOE medium range total count: 243 / NOE sequential total count: 454 / Protein phi angle constraints total count: 115 / Protein psi angle constraints total count: 120
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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