+Open data
-Basic information
Entry | Database: PDB / ID: 8wr5 | ||||||
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Title | The Crystal Structure of Mms2 from Biortus | ||||||
Components | Ubiquitin-conjugating enzyme E2 variant 2 | ||||||
Keywords | LIGASE / Ubl conjugation pathway | ||||||
Function / homology | Function and homology information error-free postreplication DNA repair / UBC13-MMS2 complex / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / positive regulation of double-strand break repair / protein K63-linked ubiquitination / regulation of DNA repair / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint ...error-free postreplication DNA repair / UBC13-MMS2 complex / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / positive regulation of double-strand break repair / protein K63-linked ubiquitination / regulation of DNA repair / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Formation of Incision Complex in GG-NER / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / protein ubiquitination / extracellular exosome / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Guo, S. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: The Crystal Structure of Mms2 from Biortus. Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Guo, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wr5.cif.gz | 45.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wr5.ent.gz | 28.9 KB | Display | PDB format |
PDBx/mmJSON format | 8wr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/8wr5 ftp://data.pdbj.org/pub/pdb/validation_reports/wr/8wr5 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16380.731 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2V2, MMS2, UEV2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15819 | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Li2SO4,0.1 M NaAC pH5.5,10% PEG 1000,10% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.953685 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 22, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953685 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→36.07 Å / Num. obs: 13856 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 713 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→33.085 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.464 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.109 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.777 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→33.085 Å
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Refine LS restraints |
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LS refinement shell |
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