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Open data
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Basic information
Entry | Database: PDB / ID: 2y9p | ||||||
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Title | Pex4p-Pex22p mutant II structure | ||||||
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![]() | LIGASE/TRANSPORT PROTEIN / LIGASE-TRANSPORT PROTEIN COMPLEX / E2 COMPLEX / ALPHA-BETA-ALPHA SANDWICH FOLD / E2 CO-ACTIVATOR | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Williams, C. / van den Berg, M. / Panjikar, S. / Distel, B. / Wilmanns, M. | ||||||
![]() | ![]() Title: Pex4P-Pex22P Structure Authors: Williams, C. / van den Berg, M. / Panjikar, S. / Distel, B. / Wilmanns, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.3 KB | Display | ![]() |
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PDB format | ![]() | 49 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.7 KB | Display | ![]() |
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Full document | ![]() | 426.2 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y9mS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19530.439 Da / Num. of mol.: 1 / Fragment: UBC DOMAIN, RESIDUES 15-183 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PCW232 / Production host: ![]() ![]() | ||
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#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.) ![]() ![]() Plasmid: PCW218 / Production host: ![]() ![]() | ||
#3: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | RESIDUE 15 IS MUTATED FROM SERINE TO ALANINE TO AID CLONING. RESIDUE ASPARAGINE 156 IS MUTATED TO ...RESIDUE 15 IS MUTATED FROM SERINE TO ALANINE TO AID CLONING. RESIDUE ASPARAGINE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.28 % / Description: NONE |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2010 / Details: SI (111) |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→47.54 Å / Num. obs: 5245 / % possible obs: 97 % / Observed criterion σ(I): 5 / Redundancy: 3.5 % / Biso Wilson estimate: 86.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 3.25→3.42 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.4 / % possible all: 79.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTY 2Y9M Resolution: 3.25→47.54 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.817 / SU B: 28.257 / SU ML: 0.48 / Cross valid method: THROUGHOUT / ESU R: 0.52 / ESU R Free: 0.591 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.638 Å2
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Refinement step | Cycle: LAST / Resolution: 3.25→47.54 Å
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Refine LS restraints |
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