+Open data
-Basic information
Entry | Database: PDB / ID: 1xt9 | ||||||
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Title | Crystal Structure of Den1 in complex with Nedd8 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Cysteine protease / ubiquitin-like / HYDROLASE-HYDROLASE INHIBITOR 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 / modification-dependent protein catabolic process / protein localization / 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 / SIR / Resolution: 2.2 Å | ||||||
Authors | Reverter, D. / Wu, K. / Erdene, T.G. / Pan, Z.Q. / Wilkinson, K.D. / Lima, C.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Structure of a Complex between Nedd8 and the Ulp/Senp Protease Family Member Den1. Authors: Reverter, D. / Wu, K. / Erdene, T.G. / Pan, Z.Q. / Wilkinson, K.D. / Lima, C.D. | ||||||
History |
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Remark 999 | SEQUENCE There is a covalent bond between CYS 163 chain A and GLY 76 chain B. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xt9.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xt9.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 1xt9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/1xt9 ftp://data.pdbj.org/pub/pdb/validation_reports/xt/1xt9 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24133.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: GLUTATHIONE S-TRANSFERASE FUSION, CLEAVED WITH THROMBIN; Gene: SENP8, FKSG8, PRSC2 / Production host: Escherichia coli (E. coli) References: UniProt: Q96LD8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Protein | Mass: 8573.978 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: GLUTATHIONE S-TRANSFERASE FUSION, CLEAVED WITH THROMBIN Gene: NEDD8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15843 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 2M ammonium sulfate, 0.1M bicine, 4% tert-butanol, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 22, 2003 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SIR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 24989 / Num. obs: 22541 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2→2.17 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 1.86 / Rsym value: 0.25 / % possible all: 85.2 |
-Processing
Software |
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Refinement | Method to determine structure: SIR / Resolution: 2.2→19.62 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1836633.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Friedel pairs were used.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.7169 Å2 / ksol: 0.3308 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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