+Open data
-Basic information
Entry | Database: PDB / ID: 2bkr | ||||||
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Title | NEDD8 NEDP1 complex | ||||||
Components |
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Keywords | PROTEIN-BINDING/HYDROLASE / PROTEIN-BINDING-HYDROLASE COMPLEX / UBIQUITIN / HYDROLASE / PROTEASE / THIOL PROTEASE / UBL CONJUGATION PATHWAY / UBIQUITIN-HYDROLASE COMPLEX | ||||||
Function / homology | Function and homology information deNEDDylase activity / protein deneddylation / regulation of proteolysis / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / cysteine-type peptidase activity / post-translational protein modification / Iron uptake and transport / protein modification process ...deNEDDylase activity / protein deneddylation / regulation of proteolysis / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / cysteine-type peptidase activity / post-translational protein modification / 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 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / 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 / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Shen, L.N. / Liu, H. / Dong, C. / Xirodimas, D. / Naismith, J.H. / Hay, R.T. | ||||||
Citation | Journal: Embo J. / Year: 2005 Title: Structural Basis of Nedd8 Ubiquitin Discrimination by the Deneddylating Enzyme Nedp1 Authors: Shen, L.N. / Liu, H. / Dong, C. / Xirodimas, D. / Naismith, J.H. / Hay, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bkr.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bkr.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 2bkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/2bkr ftp://data.pdbj.org/pub/pdb/validation_reports/bk/2bkr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24073.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q96LD8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Protein | Mass: 8661.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15843 |
#3: Water | ChemComp-HOH / |
Compound details | FUNCTION: POSSIBLE INVOLVEMENT IN THE RELEASE OF SENTRINS. POSSIBLE ROLE DURING THE EMBRYONIC ...FUNCTION: POSSIBLE INVOLVEMEN |
Sequence details | EXTRA N-TERMINAL RESIDUE FROM CLONING SER FOR CHAIN B. THE ORIGINAL SAMPLE FOR CHAIN B CONTAINS 82 ...EXTRA N-TERMINAL RESIDUE FROM CLONING SER FOR CHAIN B. THE ORIGINAL SAMPLE FOR CHAIN B CONTAINS 82 RESIDUES INCLUDING GLY GLY LEU ARG GLN (77-81) BUT THESE RESIDUES ARE CLEAVED OFF BY THE PROTEASE DURING THE COMPLEX FORMATION. THESE RESIDUES ARE NOT THEREFORE PART OF OF THE CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.1 % |
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Crystal grow | pH: 4.5 Details: CRYSTALS WERE GROWN BY SETTING-DROP METHOD BY MIXING THE NEDP1-NEDD8 COMPLEX (20MG/ML) WITH EQUAL VOLUME OF RESERVOIR SOLUTION CONTAINING 20%PEG8000, 200MM NACL, 100MM PHOSPHATE CITRATE PH4.5, pH 4.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.008 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 1, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→54 Å / Num. obs: 25411 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3 / % possible all: 83.7 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 1.9→54.23 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.177 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→54.23 Å
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