+Open data
-Basic information
Entry | Database: PDB / ID: 8svh | ||||||
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Title | Ubiquitin variant i53 mutant L67R bound to 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: 1.16 Å | ||||||
Authors | Holden, J.K. / Partridge, J.R. / 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 | 8svh.cif.gz | 122 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8svh.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 8svh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8svh_validation.pdf.gz | 436.5 KB | Display | wwPDB validaton report |
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Full document | 8svh_full_validation.pdf.gz | 440.3 KB | Display | |
Data in XML | 8svh_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 8svh_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/8svh ftp://data.pdbj.org/pub/pdb/validation_reports/sv/8svh | HTTPS FTP |
-Related structure data
Related structure data | 8svgC 8sviC 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: 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 |
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#2: Protein | Mass: 8704.019 Da / Num. of mol.: 1 / Mutation: L67R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#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: 1.89 Å3/Da / Density % sol: 34.94 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES pH6.6, 0.2 M Trimethylamine N-oxide dehydrate, 7% w/v PEG2000 |
-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 / Details: TITANIUM SILICATE FLAT MIRROR WITH PT |
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: 1.16→25.34 Å / Num. obs: 60078 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 13.55 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.03459 / Rrim(I) all: 0.0931 / Rsym value: 0.08622 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.16→1.18 Å / Mean I/σ(I) obs: 3.35 / Num. unique obs: 5857 / CC1/2: 0.873 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.16→25.34 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 17.61 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.16→25.34 Å
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LS refinement shell | Resolution: 1.16→1.18 Å
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