+Open data
-Basic information
Entry | Database: PDB / ID: 6cd9 | ||||||
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Title | GID4 in complex with a 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 / Regulation of pyruvate metabolism / 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 / MOLECULAR REPLACEMENT / Resolution: 1.55 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 | 6cd9.cif.gz | 54.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cd9.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 6cd9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/6cd9 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/6cd9 | HTTPS FTP |
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-Related structure data
Related structure data | 6ccrSC 6cctC 6ccuC 6cd8C 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 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IVV7 | ||
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#2: Protein/peptide | Mass: 545.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) synthetic construct (others) | ||
#3: Chemical | ChemComp-UNX / #4: 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: 2.11 Å3/Da / Density % sol: 41.71 % / Mosaicity: 0.19 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 24% PEG3350, 2.8% 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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Aug 16, 2016 | |||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→38.27 Å / Num. obs: 25493 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Net I/σ(I): 27.2 / Num. measured all: 168776 / 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 PDB entry 6ccr Resolution: 1.55→37.6 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.344 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 42.17 Å2 / Biso mean: 12.43 Å2 / Biso min: 5.4 Å2
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Refinement step | Cycle: final / Resolution: 1.55→37.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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