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- PDB-6izg: Solution structure of Ufm1 protein from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 6izg
TitleSolution structure of Ufm1 protein from Trypanosoma brucei
ComponentsUbiquitin-fold modifier 1
KeywordsENDOCYTOSIS / Ubiquitin like protein / stress response protein
Function / homologyUbiquitin-fold modifier 1 / Ubiquitin fold modifier 1 protein / protein modification by small protein conjugation / protein K69-linked ufmylation / Ubiquitin-like domain superfamily / mitochondrion / nucleus / cytoplasm / Ubiquitin-fold modifier 1
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodSOLUTION NMR / simulated annealing
AuthorsDiwu, Y. / Tu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31500601 China
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Solution structure of TbUfm1 from Trypanosoma brucei and its binding to TbUba5.
Authors: Diwu, Y. / Zhang, J. / Li, M. / Yang, X. / Shan, F. / Ma, H. / Zhang, X. / Liao, S. / Tu, X.
History
DepositionDec 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 2.0Oct 25, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_nmr_exptl / pdbx_nmr_software / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conf / struct_sheet_range
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl.type / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Model completeness / Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-fold modifier 1


Theoretical massNumber of molelcules
Total (without water)10,2261
Polymers10,2261
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6670 Å2
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-fold modifier 1


Mass: 10225.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb927.8.5380 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57UL0

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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 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 1.5 mM [U-13C; U-15N] Ufm1, 150 mM sodium chloride, 20 mM sodium phosphate, 2 mM EDTA, 2 mM DTT, 90% H2O/10% D2O
Label: 13C-15N / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMUfm1[U-13C; U-15N]1
150 mMsodium chloridenatural abundance1
20 mMsodium phosphatenatural abundance1
2 mMEDTAnatural abundance1
2 mMDTTnatural abundance1
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 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
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxcollection
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
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

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