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Yorodumi- PDB-2mrp: NMR solution structure of the Ubiquitin like domain (UBL) of DNA-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mrp | ||||||
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Title | NMR solution structure of the Ubiquitin like domain (UBL) of DNA-damage-inducible 1 protein (Ddi1) | ||||||
Components | DNA damage-inducible protein 1 | ||||||
Keywords | UBIQUITIN-BINDING PROTEIN / DNA-damage-inducible 1 protein / Ddi1 / Ubiquitin like domain / UBL / Ubiquitin binding | ||||||
Function / homology | Function and homology information proteasome regulatory particle binding / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / polyubiquitin modification-dependent protein binding / protein secretion / vesicle-mediated transport / SNARE binding / positive regulation of DNA replication / ubiquitin binding / protein-macromolecule adaptor activity ...proteasome regulatory particle binding / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / polyubiquitin modification-dependent protein binding / protein secretion / vesicle-mediated transport / SNARE binding / positive regulation of DNA replication / ubiquitin binding / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / aspartic-type endopeptidase activity / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Nowicka, U. / Fushman, D. / Chen, T. | ||||||
Citation | Journal: Structure / Year: 2015 Title: DNA-Damage-Inducible 1 Protein (Ddi1) Contains an Uncharacteristic Ubiquitin-like Domain that Binds Ubiquitin. Authors: Nowicka, U. / Zhang, D. / Walker, O. / Krutauz, D. / Castaneda, C.A. / Chaturvedi, A. / Chen, T.Y. / Reis, N. / Glickman, M.H. / Fushman, D. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mrp.cif.gz | 244.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mrp.ent.gz | 209.2 KB | Display | PDB format |
PDBx/mmJSON format | 2mrp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/2mrp ftp://data.pdbj.org/pub/pdb/validation_reports/mr/2mrp | HTTPS FTP |
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-Related structure data
Related structure data | 2mr9C 2mroC 2mwsC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10589.902 Da / Num. of mol.: 1 Fragment: Ubiquitin like domain of DNA-damage-inducible 1 protein (Ddi1UBL) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: DDI1, VSM1, YER143W / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P40087 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 10 / Conformers submitted total number: 10 |