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- PDB-5zew: A ubiquitin-like protein from the hyperthermophilic archaea Caldi... -

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Basic information

Entry
Database: PDB / ID: 5zew
TitleA ubiquitin-like protein from the hyperthermophilic archaea Caldiarchaeum subterraneum
ComponentsUbiquitin-like protein
KeywordsSTRUCTURAL PROTEIN / ubiquitin-like protein
Function / homology
Function and homology information


polyubiquitin modification-dependent protein binding / ubiquitin-dependent protein catabolic process / metal ion binding / cytosol
Similarity search - Function
: / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-like protein
Similarity search - Component
Biological speciesCandidatus Caldiarchaeum subterraneum (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsMi, J. / Ye, K.Q.
CitationJournal: To Be Published
Title: The hydrophobic effect and electrostatic interactions contribute to the thermostability of the ubiquitin-like protein from the hyperthermophilic archaea Caldiarchaeum subterraneum
Authors: Mi, J. / Ye, K.Q. / Ni, J. / Zhang, J.H. / Liao, S.H. / Tu, X.M.
History
DepositionFeb 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-like protein


Theoretical massNumber of molelcules
Total (without water)8,1081
Polymers8,1081
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 area5490 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin-like protein


Mass: 8107.555 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-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D C(CO)NH
151isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solid
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: 6.7 / 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
Amber14CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, DUKE, LUO, ... AND KOLLMANrefinement
CYANA3structure solution
Sparkystructure solution
NMRDrawstructure solution
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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