+Open data
-Basic information
Entry | Database: PDB / ID: 4fh1 | ||||||
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Title | S. cerevisiae Ubc13-N79A | ||||||
Components | Ubiquitin-conjugating enzyme E2 13 | ||||||
Keywords | LIGASE / Ubiquitin Conjugating Enzyme | ||||||
Function / homology | Function and homology information protein targeting to vacuolar membrane / Aggrephagy / ubiquitin conjugating enzyme complex / free ubiquitin chain polymerization / fungal-type vacuole membrane / postreplication repair / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein polyubiquitination ...protein targeting to vacuolar membrane / Aggrephagy / ubiquitin conjugating enzyme complex / free ubiquitin chain polymerization / fungal-type vacuole membrane / postreplication repair / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein polyubiquitination / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å | ||||||
Authors | Berndsen, C.E. / Wolberger, C. / Wiener, R. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2013 Title: A conserved asparagine has a structural role in ubiquitin-conjugating enzymes. Authors: Berndsen, C.E. / Wiener, R. / Yu, I.W. / Ringel, A.E. / Wolberger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fh1.cif.gz | 42.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fh1.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 4fh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/4fh1 ftp://data.pdbj.org/pub/pdb/validation_reports/fh/4fh1 | HTTPS FTP |
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-Related structure data
Related structure data | 1jbbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17430.893 Da / Num. of mol.: 1 / Mutation: N79A, C87S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: UBC13, YDR092W, YD6652.04 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P52490, ubiquitin-protein ligase |
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#2: Chemical | ChemComp-NHE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.37 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 10.3 Details: 0.1 M CHES, pH 10.3, 20% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→66.71 Å / Num. obs: 7065 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rsym value: 0.139 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.65→2.7 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JBB Resolution: 2.61→33.35 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.926 / SU B: 9.487 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.387 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 56.209 Å2
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Refinement step | Cycle: LAST / Resolution: 2.61→33.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.607→2.674 Å / Total num. of bins used: 20
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