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- PDB-5kgq: NMR structure and dynamics of Q4DY78, a conserved kinetoplasid-sp... -

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Basic information

Entry
Database: PDB / ID: 5kgq
TitleNMR structure and dynamics of Q4DY78, a conserved kinetoplasid-specific protein from Trypanosoma cruzi
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / hypothetical protein / conserved
Function / homologyUncharacterized protein
Function and homology information
Biological speciesTrypanosoma cruzi (eukaryote)
MethodSOLUTION NMR / simulated annealing
AuthorsD'Andrea, E.D. / Retel, J.S. / Diehl, A. / Schmieder, P. / Oschkinat, H. / Pires, J.R.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)141688/2011-4 Brazil
CAPES99999.011648/2013-09 Brazil
CitationJournal: J.Struct.Biol. / Year: 2021
Title: NMR structure and dynamics of Q4DY78, a conserved kinetoplasid-specific protein from Trypanosoma cruzi.
Authors: D'Andrea, E.D. / Retel, J.S. / Diehl, A. / Schmieder, P. / Oschkinat, H. / Pires, J.R.
History
DepositionJun 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Revision 1.5Jun 12, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,5261
Polymers12,5261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 12526.128 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: CL Brener / Gene: Tc00.1047053511907.89 / Plasmid: pGEX-4T2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: Q4DY78

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
212isotropic12D 1H-15N HSQC
323isotropic22D 1H-13C HSQC
131isotropic12D 1H-1H TOCSY
141isotropic12D 1H-1H NOESY
353isotropic23D CBCA(CO)NH
363isotropic23D HN(CA)CB
272isotropic13D HBHA(CO)NH
282isotropic13D 1H-15N TOCSY
393isotropic13D (H)CCH-COSY
3103isotropic23D (H)CCH-TOCSY
3113isotropic13D HNCO
2122isotropic23D 1H-15N NOESY
3133isotropic23D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.4 mM Unlabeled Q4DY78, 90% H2O/10% D2OUnlabeled, 0.4 mM, PBS buffer (10 mM Na2HPO4, 1.8 mM KH2PO4, 140 mM NaCl, 2.7 mM KCl), pH 7.4, added 10 mM DTTUnlabeled90% H2O/10% D2O
solution20.3 mM [U-100% 15N] Q4DY78, 90% H2O/10% D2O15N labeled, 0.3 mM, PBS buffer (10 mM Na2HPO4, 1.8 mM KH2PO4, 140 mM NaCl, 2.7 mM KCl), pH 7.4, added 10 mM DTT15N labeled90% H2O/10% D2O
solution30.8 mM [U-100% 13C; U-100% 15N] Q4DY78, 90% H2O/10% D2O13C, 15N double-labeled, 0.8 mM, in PBS buffer (10 mM Na2HPO4, 1.8 mM KH2PO4, 140 mM NaCl, 2.7 mM KCl), pH 7.4, added 10 mM DTT13C, 15N double-labeled90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMQ4DY78Unlabeled1
0.3 mMQ4DY78[U-100% 15N]2
0.8 mMQ4DY78[U-100% 13C; U-100% 15N]3
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1Unlabeled, 0.4 mM, PBS buffer (10 mM Na2HPO4, 1.8 mM KH2PO4, 140 mM NaCl, 2.7 mM KCl), pH 7.4, added 10 mM DTT10 mM Na2HPO4, 1.8 mM KH2PO4, 140 mM NaCl, 2.7 mM KCl mMunlabeled7.41 atm298 K
215N labeled, 0.3 mM, PBS buffer (10 mM Na2HPO4, 1.8 mM KH2PO4, 140 mM NaCl, 2.7 mM KCl), pH 7.4, added 10 mM DTT10 mM Na2HPO4, 1.8 mM KH2PO4, 140 mM NaCl, 2.7 mM KCl mM15N labeled7.41 atm298 K
313C, 15N double-labeled, 0.8 mM, in PBS buffer (10 mM Na2HPO4, 1.8 mM KH2PO4, 140 mM NaCl, 2.7 mM KCl), pH 7.4, added 10 mM DTT10 mM Na2HPO4, 1.8 mM KH2PO4, 140 mM NaCl, 2.7 mM KCl mM13C, 15N double-labeled7.41 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III8001Triple resonance probe
Bruker AVANCE IIIBrukerAVANCE III6002Triple resonance cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1Bruker Biospincollection
TopSpin3.1Bruker Biospinprocessing
Sparky3.114Goddardpeak picking
Sparky3.114Goddardchemical shift assignment
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
Details: structures are based on a total of 2387 restraints, 2171 are NOE-derived distance constraints, 144 dihedral angle restraints, 72 distance restraints from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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