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Open data
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Basic information
Entry | Database: PDB / ID: 8svg | ||||||
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Title | Ubiquitin variant i53 in complex with 53BP1 Tudor domain | ||||||
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![]() | PROTEIN BINDING / inhibitor | ||||||
Function / homology | ![]() DNA damage checkpoint signaling / histone binding / nuclear body / positive regulation of transcription by RNA polymerase II / nucleoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Holden, J.K. / Partridge, J.R. / Wibowo, A.S. / Mulichak, A. | ||||||
Funding support | 1items
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121 KB | Display | ![]() |
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PDB format | ![]() | 70.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.3 KB | Display | ![]() |
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Full document | ![]() | 435.4 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8svhC ![]() 8sviC ![]() 8svjC ![]() 8t2dC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() ![]() ![]() |
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#2: Protein | Mass: 8659.982 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 0.1 M MES pH 6.4, 0.2 M Trimethylamine N-oxide dehydrate, 2% w/v PEG2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.21→25.33 Å / Num. obs: 51451 / % possible obs: 96.93 % / Redundancy: 7.5 % / Biso Wilson estimate: 12.28 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.02066 / Rrim(I) all: 0.05672 / Rsym value: 0.05269 / Net I/σ(I): 18.68 |
Reflection shell | Resolution: 1.21→1.23 Å / Redundancy: 7.5 % / Num. unique obs: 4865 / CC1/2: 0.952 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 16.47 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.21→25.3 Å
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LS refinement shell | Resolution: 1.21→1.23 Å
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