+Open data
-Basic information
Entry | Database: PDB / ID: 2bep | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ubiquitin conjugating enzyme E2-25K | ||||||
Components | UBIQUITIN-CONJUGATING ENZYME E2-25 KDA | ||||||
Keywords | LIGASE / UBIQUITIN / E2 CONJUGATING ENZYME / PROTEIN DEGRADATION / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein polyubiquitination / ubiquitin-protein transferase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / ATP binding ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein polyubiquitination / ubiquitin-protein transferase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Pichler, A. / Knipscheer, P. / Oberhofer, E. / Van Dijk, W.J. / Korner, R. / Velgaard Olsen, J. / Jentsch, S. / Melchior, F. / Sixma, T.K. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2005 Title: Sumo Imodification of the Ubiquitin Conjugating Enzyme E2-25K Authors: Pichler, A. / Knipscheer, P. / Oberhofer, E. / Van Dijk, W.J. / Korner, R. / Velgaard Olsen, J. / Jentsch, S. / Melchior, F. / Sixma, T.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2bep.cif.gz | 52.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2bep.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/2bep ftp://data.pdbj.org/pub/pdb/validation_reports/be/2bep | HTTPS FTP |
---|
-Related structure data
Related structure data | 2bf8C 1fzyS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17846.412 Da / Num. of mol.: 1 / Fragment: CONSERVED CORE DOMAIN, RESIDUES 1-155 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61085, ubiquitin-protein ligase |
---|---|
#2: Chemical | ChemComp-BME / |
#3: Water | ChemComp-HOH / |
Compound details | ATP + UBIQUITIN + PROTEIN LYSINE = AMP + DIPHOSPHAT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 20 |
---|
-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.7 % |
---|---|
Crystal grow | pH: 8.5 Details: 100 MM TRIS PH 8.0 70 MM AMMONIUM SULFATE 17 % PEGMME 5000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 8, 2003 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 19623 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.08 / Rsym value: 0.072 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.548 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FZY Resolution: 1.8→51.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.418 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.116 / 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: 24.61 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→51.3 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|