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Yorodumi- PDB-5zew: A ubiquitin-like protein from the hyperthermophilic archaea Caldi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zew | ||||||
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Title | A ubiquitin-like protein from the hyperthermophilic archaea Caldiarchaeum subterraneum | ||||||
Components | Ubiquitin-like protein | ||||||
Keywords | STRUCTURAL 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 | ||||||
Biological species | Candidatus Caldiarchaeum subterraneum (archaea) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Mi, J. / Ye, K.Q. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zew.cif.gz | 455.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zew.ent.gz | 382.9 KB | Display | PDB format |
PDBx/mmJSON format | 5zew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zew_validation.pdf.gz | 397.3 KB | Display | wwPDB validaton report |
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Full document | 5zew_full_validation.pdf.gz | 480.4 KB | Display | |
Data in XML | 5zew_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 5zew_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/5zew ftp://data.pdbj.org/pub/pdb/validation_reports/ze/5zew | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: 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 |
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Sample | Conc.: 0.5 mM / Component: ubiquitin-like protein / Isotopic labeling: [U-99% 13C; U-99% 15N] |
Sample conditions | Ionic strength: 120 mM / Label: conditions_1 / pH: 6.7 / Pressure: 1 atm / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 5 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |