+Open data
-Basic information
Entry | Database: PDB / ID: 6xoq | ||||||
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Title | DCN1 covalently bound to inhibitor 4 | ||||||
Components | Lysozyme, DCN1-like protein 1 chimera | ||||||
Keywords | LIGASE/LIGASE INHIBITOR / Inhibitor / LIGASE / LIGASE-LIGASE INHIBITOR complex | ||||||
Function / homology | Function and homology information positive regulation of protein neddylation / ubiquitin-like protein binding / regulation of protein neddylation / protein neddylation / ubiquitin conjugating enzyme binding / cullin family protein binding / regulation of protein ubiquitination / ubiquitin ligase complex / viral release from host cell by cytolysis / peptidoglycan catabolic process ...positive regulation of protein neddylation / ubiquitin-like protein binding / regulation of protein neddylation / protein neddylation / ubiquitin conjugating enzyme binding / cullin family protein binding / regulation of protein ubiquitination / ubiquitin ligase complex / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / Neddylation / host cell cytoplasm / defense response to bacterium / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.07 Å | ||||||
Authors | Stuckey, J.A. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Selective inhibition of cullin 3 neddylation through covalent targeting DCN1 protects mice from acetaminophen-induced liver toxicity. Authors: Zhou, H. / Lu, J. / Chinnaswamy, K. / Stuckey, J.A. / Liu, L. / McEachern, D. / Yang, C.Y. / Bernard, D. / Shen, H. / Rui, L. / Sun, Y. / Wang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xoq.cif.gz | 168.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xoq.ent.gz | 129.2 KB | Display | PDB format |
PDBx/mmJSON format | 6xoq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/6xoq ftp://data.pdbj.org/pub/pdb/validation_reports/xo/6xoq | HTTPS FTP |
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-Related structure data
Related structure data | 6xolC 6xomC 6xonC 6xooC 6xopC 5v83S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 44347.434 Da / Num. of mol.: 1 / Mutation: C54T,C97A,D127A,A146T,R154A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human) Gene: e, T4Tp126, DCUN1D1, DCN1, DCUN1L1, RP42, SCCRO / Production host: Escherichia coli (E. coli) / References: UniProt: D9IEF7, UniProt: Q96GG9, lysozyme |
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#2: Chemical | ChemComp-H9S / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-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: 41.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 28-33% PEG 3350, 0.2 M ammonium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 7, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.07→50 Å / Num. obs: 23754 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 25.95 Å2 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Χ2: 0.942 / Net I/σ(I): 13.9 / Num. measured all: 166845 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5V83 Resolution: 2.07→35.77 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.905 / SU R Cruickshank DPI: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.252 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.188
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Displacement parameters | Biso max: 98.88 Å2 / Biso mean: 31.02 Å2 / Biso min: 8.22 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.07→35.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.07→2.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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