+
Open data
-
Basic information
Entry | Database: PDB / ID: 6cct | ||||||
---|---|---|---|---|---|---|---|
Title | Fragment of GID4 in complex with a short peptide | ||||||
![]() |
| ||||||
![]() | PEPTIDE BINDING PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() protein catabolic process in the vacuole / GID complex / protein targeting to vacuole / negative regulation of gluconeogenesis / ubiquitin ligase complex / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dong, C. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 79.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 58.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 425.4 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 9.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ccrSC ![]() 6ccuC ![]() 6cd8C ![]() 6cd9C ![]() 6cdcC ![]() 6cdgC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() |
---|---|
#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: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40 % / Mosaicity: 0.23 ° |
---|---|
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 | |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||
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
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→39.3 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|