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- PDB-2mqj: Solution structure of ubiquitin-like protein from Caldiarchaeum s... -

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Basic information

Entry
Database: PDB / ID: 2mqj
TitleSolution structure of ubiquitin-like protein from Caldiarchaeum subterraneum
ComponentsUbiquitin-like protein
KeywordsLIGASE / Caldiarchaeum subterraneum
Function / homology
Function and homology information


polyubiquitin modification-dependent protein binding / ubiquitin-dependent protein catabolic process / metal ion binding / cytosol
Similarity search - Function
: / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 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
Ubiquitin-like protein
Similarity search - Component
Biological speciesCandidatus Caldiarchaeum subterraneum (archaea)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model1
AuthorsYe, K.
CitationJournal: To be Published
Title: Solution structure of ubiquitin-like protein from Caldiarchaeum subterraneum
Authors: Ye, K.
History
DepositionJun 22, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Atomic model / Database references / Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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 / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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: Ubiquitin-like protein


Theoretical massNumber of molelcules
Total (without water)9,2591
Polymers9,2591
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin-like protein


Mass: 9258.878 Da / Num. of mol.: 1 / Fragment: UNP residues 1-77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Caldiarchaeum subterraneum (archaea)
Gene: CSUB_C1474, HGMM_F04B03C03, HGMM_F21D07C21, HGMM_F30C12C33
Production host: Escherichia coli (E. coli) / References: UniProt: E6N8B8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D H(CCO)NH
1713D 1H-15N NOESY

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Sample preparation

DetailsContents: 1mM [U-100% 13C; U-100% 15N] sodium phosphate-1, 1mM [U-100% 15N] sodium phosphate-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMsodium phosphate-1[U-100% 13C; U-100% 15N]1
1 mMsodium phosphate-2[U-100% 15N]1
Sample conditionsIonic strength: 0.1 / 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
SparkyGoddardchemical shift assignment
Sparkyrefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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