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- PDB-5zmb: A-ubiquitin like protein from the trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 5zmb
TitleA-ubiquitin like protein from the trypanosoma brucei
Componentsubiquintin-like protein
KeywordsPROTEIN BINDING / STRUCTURE FROM CYANA 3.0
Function / homologyaxoneme / Ubiquitin-like domain superfamily / Ubiquitin-like domain-containing protein
Function and homology information
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodSOLUTION NMR / distance geometry
AuthorsMi, J. / Tu, X.M.
CitationJournal: Protein Sci. / Year: 2018
Title: Solution structure of a ubiquitin-like protein from Trypanosoma brucei
Authors: Mi, J. / Zhang, J. / Liao, S. / Tu, X.
History
DepositionApr 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.3May 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: ubiquintin-like protein


Theoretical massNumber of molelcules
Total (without water)9,1411
Polymers9,1411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6170 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #11

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Components

#1: Protein ubiquintin-like protein


Mass: 9141.467 Da / Num. of mol.: 1 / Fragment: UNP residues 1-81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb927.6.3140
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q583M0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D C(CO)NH
151isotropic13D 1H-15N NOESY
161isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-99% 13C; U-99% 15N] ubiquitin-like protein, 90% H2O/10% D2O
Label: 15N_13C sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: ubiquitin-like protein / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 120 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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