+Open data
-Basic information
Entry | Database: PDB / ID: 1ndd | ||||||
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Title | STRUCTURE OF NEDD8 | ||||||
Components | PROTEIN (UBIQUITIN-LIKE PROTEIN NEDD8) | ||||||
Keywords | SIGNALING PROTEIN / NEDD8 / NEDD-8 / UBIQUITIN-LIKE / PROTEOLYSIS | ||||||
Function / homology | Function and homology information regulation of proteolysis / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / Iron uptake and transport / protein modification process / protein localization / modification-dependent protein catabolic process / protein tag activity / UCH proteinases ...regulation of proteolysis / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / Iron uptake and transport / protein modification process / protein localization / modification-dependent protein catabolic process / protein tag activity / UCH proteinases / Cargo recognition for clathrin-mediated endocytosis / Neddylation / ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / proteolysis / extracellular exosome / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Whitby, F.G. / Xia, G. / Pickart, C.M. / Hill, C.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Crystal structure of the human ubiquitin-like protein NEDD8 and interactions with ubiquitin pathway enzymes. Authors: Whitby, F.G. / Xia, G. / Pickart, C.M. / Hill, C.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ndd.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ndd.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ndd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ndd_validation.pdf.gz | 455 KB | Display | wwPDB validaton report |
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Full document | 1ndd_full_validation.pdf.gz | 456.7 KB | Display | |
Data in XML | 1ndd_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 1ndd_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/1ndd ftp://data.pdbj.org/pub/pdb/validation_reports/nd/1ndd | HTTPS FTP |
-Related structure data
Related structure data | 1ubqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 8573.978 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: HUMAN NEDD8 UBIQUITIN-LIKE PROTEIN MONOMER WITH 4 MOLECULES IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT Source: (gene. exp.) Homo sapiens (human) / Description: EXPRESSED IN E.COLI / Plasmid: PET3A-NEDD8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q15843 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.8 / Details: pH 4.8 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 41 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 7.6 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 36579 / % possible obs: 97.8 % / Observed criterion σ(I): -2 / Redundancy: 6.9 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.452 / % possible all: 93.7 |
Reflection | *PLUS Num. measured all: 232354 |
Reflection shell | *PLUS % possible obs: 93.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UBQ Resolution: 1.6→100 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 23.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.67 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 3 % / Rfactor Rfree: 0.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.46 / % reflection Rfree: 3.7 % / Rfactor Rwork: 0.428 |