+Open data
-Basic information
Entry | Database: PDB / ID: 6cct | ||||||
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Title | Fragment of GID4 in complex with a short peptide | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Vacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / ubiquitin ligase complex / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / Glucose-induced degradation protein 4 homolog Function and homology information | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Dong, C. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2018 Title: Molecular basis of GID4-mediated recognition of degrons for the Pro/N-end rule pathway. Authors: Dong, C. / Zhang, H. / Li, L. / Tempel, W. / Loppnau, P. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cct.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cct.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 6cct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/6cct ftp://data.pdbj.org/pub/pdb/validation_reports/cc/6cct | HTTPS FTP |
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-Related structure data
Related structure data | 6ccrSC 6ccuC 6cd8C 6cd9C 6cdcC 6cdgC S: Starting model for refinement C: citing same article (ref.) |
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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: 19604.777 Da / Num. of mol.: 1 / Fragment: residues 124-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GID4, C17orf39, VID24 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IVV7 |
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#2: Protein/peptide | Mass: 428.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40 % / Mosaicity: 0.23 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 20% PEG3350, 2% Tacsimate pH 7.0 and 0.1M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2017 | |||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→101.67 Å / Num. obs: 10614 / % possible obs: 100 % / Redundancy: 11.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.016 / Rrim(I) all: 0.053 / Net I/σ(I): 22.4 / Num. measured all: 125391 / Scaling rejects: 0 | |||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: early version of model from PDB entry 6CCR Resolution: 2.4→39.3 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.935 / SU B: 18.466 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.52 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The rotamer of peptide residue T2 was not clearly resolved by electron density, but chosen so as to enable plausible interactions with surrounding atoms of the model.
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.05 Å2 / Biso mean: 60.158 Å2 / Biso min: 38.87 Å2
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Refinement step | Cycle: final / Resolution: 2.4→39.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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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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