+Open data
-Basic information
Entry | Database: PDB / ID: 2y9m | ||||||
---|---|---|---|---|---|---|---|
Title | Pex4p-Pex22p structure | ||||||
Components |
| ||||||
Keywords | LIGASE/TRANSPORT PROTEIN / LIGASE-TRANSPORT PROTEIN COMPLEX / UBIQUITIN CONJUGATING ENZYME / E2 COMPLEX / PEROXISOMAL PROTEIN / ALPHA-BETA-ALPHA SANDWICH FOLD / E2 CO-ACTIVATOR | ||||||
Function / homology | Function and homology information protein import into peroxisome matrix, receptor recycling / peroxisome organization / ubiquitin-protein transferase activator activity / positive regulation of protein autoubiquitination / peroxisomal membrane / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein autoubiquitination / positive regulation of protein ubiquitination ...protein import into peroxisome matrix, receptor recycling / peroxisome organization / ubiquitin-protein transferase activator activity / positive regulation of protein autoubiquitination / peroxisomal membrane / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein autoubiquitination / positive regulation of protein ubiquitination / protein polyubiquitination / ubiquitin-protein transferase activity / peroxisome / protein ubiquitination / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | ||||||
Authors | Williams, C. / van den Berg, M. / Panjikar, S. / Distel, B. / Wilmanns, M. | ||||||
Citation | Journal: Embo J. / Year: 2011 Title: Insights Into Ubiquitin-Conjugating Enzyme/ Co-Activator Interactions from the Structure of the Pex4P:Pex22P Complex. Authors: Williams, C. / van den Berg, M. / Panjikar, S. / Stanley, W.A. / Distel, B. / Wilmanns, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2y9m.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2y9m.ent.gz | 101.3 KB | Display | PDB format |
PDBx/mmJSON format | 2y9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y9m_validation.pdf.gz | 450.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2y9m_full_validation.pdf.gz | 452.7 KB | Display | |
Data in XML | 2y9m_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 2y9m_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/2y9m ftp://data.pdbj.org/pub/pdb/validation_reports/y9/2y9m | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19573.463 Da / Num. of mol.: 1 / Fragment: UBC DOMAIN, RESIDUES 15-183 / Mutation: YES Source method: isolated from a genetically manipulated source Details: DISULPHIDE BOND BETWEEN RESIDUES 105 AND 146 Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PCW187 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P29340, ubiquitin-protein ligase | ||||||
---|---|---|---|---|---|---|---|
#2: Protein | Mass: 14439.574 Da / Num. of mol.: 1 / Fragment: SOLUBLE DOMAIN, RESIDUES 54-180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PCW218 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P39718 | ||||||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | RESIDUE 15 IS MUTATED FROM SERINE TO ALANINE TO AID CLONING. THE N-TERMINAL GLYCINE IS LEFT OVER ...RESIDUE 15 IS MUTATED FROM SERINE TO ALANINE TO AID CLONING. THE N-TERMINAL GLYCINE IS LEFT OVER FROM THE TAG THE N-TERMINAL GLYCINE AND ALANINE ARE LEFT OVER FROM THE TAG | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.46 % Description: A 4 WAVELENGTH MAD DATA SET WAS COLLECTED AND THE MODEL FROM THIS DATASET WAS USED AS MR MODEL FOR THE NATIVE DATASET |
---|---|
Crystal grow | pH: 7 Details: 8.0 % (V/V) ETHYLENE GLYCOL, 14.0 % (W/V) POLYETHYLENE GLYCOL, 0.1 M HEPES PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2008 / Details: DIAMOND 111 |
Radiation | Monochromator: DIAMOND 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→34.7 Å / Num. obs: 11039 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.8 / % possible all: 99.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.897 / SU B: 22.417 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.321 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.852 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|