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- PDB-2lrw: Solution structure of a ubiquitin-like protein from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 2lrw
TitleSolution structure of a ubiquitin-like protein from Trypanosoma brucei
ComponentsUbiquitin, putative
KeywordsCELL CYCLE / POSTTRANSLATIONAL PROTEIN MODIFIER
Function / homology
Function and homology information


protein neddylation / regulation of proteolysis / modification-dependent protein catabolic process / protein tag activity / cilium / ubiquitin protein ligase binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsWang, R. / Wang, T. / Liao, S. / Zhang, J. / Tu, X.
CitationJournal: To be Published
Title: Solution structure of a ubiqutin-like protein from Trypanosoma bucei
Authors: Wang, R. / Liao, S. / Wang, T. / Zhang, J. / Tu, X.
History
DepositionApr 13, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / 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 / _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: Ubiquitin, putative


Theoretical massNumber of molelcules
Total (without water)9,5091
Polymers9,5091
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 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin, putative


Mass: 9509.005 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb927.4.2540 / Production host: Escherichia coli (E. coli) / References: UniProt: Q584D3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HN(CA)CB
1613D H(CCO)NH
1713D HBHA(CO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] tbubl-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: tbubl-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.15 / pH: 6.8 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichchemical shift calculation
CYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20 / Representative conformer: 1

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