+Open data
-Basic information
Entry | Database: PDB / ID: 8svi | ||||||
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Title | Ubiquitin variant i53:Mutant L67H with 53BP1 Tudor domain | ||||||
Components |
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Keywords | PROTEIN BINDING / Inhibitor | ||||||
Function / homology | Function and homology information DNA damage checkpoint signaling / histone binding / nuclear body / positive regulation of transcription by RNA polymerase II / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Partridge, J.R. / Holden, J.K. / Wibowo, A.S. / Mulichak, A. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Functional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair. Authors: Perez-Bermejo, J.A. / Efagene, O. / Matern, W.M. / Holden, J.K. / Kabir, S. / Chew, G.M. / Andreoletti, G. / Catton, E. / Ennis, C.L. / Garcia, A. / Gerstenberg, T.L. / Hill, K.A. / Jain, A. ...Authors: Perez-Bermejo, J.A. / Efagene, O. / Matern, W.M. / Holden, J.K. / Kabir, S. / Chew, G.M. / Andreoletti, G. / Catton, E. / Ennis, C.L. / Garcia, A. / Gerstenberg, T.L. / Hill, K.A. / Jain, A. / Krassovsky, K. / Lalisan, C.D. / Lord, D. / Quejarro, B.J. / Sales-Lee, J. / Shah, M. / Silva, B.J. / Skowronski, J. / Strukov, Y.G. / Thomas, J. / Veraz, M. / Vijay, T. / Wallace, K.A. / Yuan, Y. / Grogan, J.L. / Wienert, B. / Lahiri, P. / Treusch, S. / Dever, D.P. / Soros, V.B. / Partridge, J.R. / Seim, K.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8svi.cif.gz | 123 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8svi.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 8svi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8svi_validation.pdf.gz | 447.2 KB | Display | wwPDB validaton report |
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Full document | 8svi_full_validation.pdf.gz | 450.1 KB | Display | |
Data in XML | 8svi_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 8svi_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/8svi ftp://data.pdbj.org/pub/pdb/validation_reports/sv/8svi | HTTPS FTP |
-Related structure data
Related structure data | 8svgC 8svhC 8svjC 8t2dC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8684.972 Da / Num. of mol.: 1 / Mutation: L67H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Production host: Escherichia coli O111:NM str. 01-3076 (bacteria) |
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#2: Protein | Mass: 13916.683 Da / Num. of mol.: 1 / Fragment: Tudor Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Production host: Escherichia coli (E. coli) / References: UniProt: A6NNK5 |
#3: Chemical | ChemComp-GOL / |
#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: 1.88 Å3/Da / Density % sol: 34.52 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES pH 6.0, 0.2 M Trimethylamine N-oxide dehydrate, 11% w/v PEG MME 2000 |
-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: 0.95372 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 8, 2022 |
Radiation | Monochromator: DOUBLE CRYSTAL / MULTILAYER MONOCHROMATOR SI(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→25.21 Å / Num. obs: 59957 / % possible obs: 98 % / Redundancy: 7 % / Biso Wilson estimate: 13.83 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.03447 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.15→1.17 Å / Rmerge(I) obs: 0.9862 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 5255 / CC1/2: 0.558 / % possible all: 86.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→25.21 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 15.26 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→25.21 Å
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LS refinement shell | Resolution: 1.15→1.17 Å
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