[English] 日本語
Yorodumi- PDB-3ceg: Crystal structure of the UBC domain of baculoviral IAP repeat-con... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ceg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the UBC domain of baculoviral IAP repeat-containing protein 6 | ||||||
Components | Baculoviral IAP repeat-containing protein 6 | ||||||
Keywords | LIGASE / APOPTOSIS / PROTEASE INHIBITOR / THIOL PROTEASE INHIBITOR / UBL CONJUGATION PATHWAY / STRUCTURAL GENOMICS CONSORTIUM / SGC | ||||||
Function / homology | Function and homology information spongiotrophoblast layer development / labyrinthine layer development / ALK mutants bind TKIs / Flemming body / microtubule organizing center / cysteine-type endopeptidase inhibitor activity / ubiquitin conjugating enzyme activity / regulation of cytokinesis / negative regulation of extrinsic apoptotic signaling pathway / RING-type E3 ubiquitin transferase ...spongiotrophoblast layer development / labyrinthine layer development / ALK mutants bind TKIs / Flemming body / microtubule organizing center / cysteine-type endopeptidase inhibitor activity / ubiquitin conjugating enzyme activity / regulation of cytokinesis / negative regulation of extrinsic apoptotic signaling pathway / RING-type E3 ubiquitin transferase / trans-Golgi network / spindle pole / ubiquitin-protein transferase activity / Signaling by ALK fusions and activated point mutants / regulation of cell population proliferation / midbody / cell population proliferation / protein ubiquitination / endosome / cell cycle / cell division / protein phosphorylation / centrosome / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.008 Å | ||||||
Authors | Walker, J.R. / Avvakumov, G.V. / Xue, S. / Butler-Cole, C. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Mol Cell Proteomics / Year: 2012 Title: A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen. Authors: Sheng, Y. / Hong, J.H. / Doherty, R. / Srikumar, T. / Shloush, J. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Neculai, D. / Wan, J.W. / Kim, S.K. / Arrowsmith, C.H. / Raught, B. / Dhe-Paganon, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ceg.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ceg.ent.gz | 106.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ceg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ceg_validation.pdf.gz | 432.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ceg_full_validation.pdf.gz | 436.5 KB | Display | |
Data in XML | 3ceg_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 3ceg_validation.cif.gz | 36.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/3ceg ftp://data.pdbj.org/pub/pdb/validation_reports/ce/3ceg | HTTPS FTP |
-Related structure data
Related structure data | 1y6lC 1yh2C 1yrvC 1zdnC 1zuoC 2a4dC 2a7lC 2awfC 2f4wC 2ob4C 2qgxC 2z5dC 3bzhC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37055.660 Da / Num. of mol.: 2 / Fragment: UBC domain: Residues 4470-4792 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC6, KIAA1289 / Plasmid: pET28-MHL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NR09, ubiquitin-protein ligase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.3 % |
---|---|
Crystal grow | Temperature: 298 K / pH: 10 Details: 11 % PEG 8000, 0.1 M Gycine buffer pH 10.0, 0.001 M DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97942 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2008 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 62447 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rsym value: 0.114 / Net I/σ(I): 18.623 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.585 / Rsym value: 0.637 / % possible all: 70.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.008→44.5 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.118 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.563 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.008→44.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.008→2.06 Å / Total num. of bins used: 20
|