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- PDB-8svg: Ubiquitin variant i53 in complex with 53BP1 Tudor domain -

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Basic information

Entry
Database: PDB / ID: 8svg
TitleUbiquitin variant i53 in complex with 53BP1 Tudor domain
Components
  • Tumor protein p53 binding protein 1
  • Ubiquitin variant i53
KeywordsPROTEIN BINDING / inhibitor
Function / homology
Function and homology information


nuclear body / DNA damage response / nucleoplasm
Similarity search - Function
Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
Tumor protein p53 binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsHolden, J.K. / Partridge, J.R. / Wibowo, A.S. / Mulichak, A.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: 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
DepositionMay 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Refinement description / Category: citation / citation_author / refine_ls_shell
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor protein p53 binding protein 1
B: Ubiquitin variant i53


Theoretical massNumber of molelcules
Total (without water)22,5772
Polymers22,5772
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-8 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.37, 46.86, 90.32
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tumor protein p53 binding protein 1


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
#2: Protein Ubiquitin variant i53


Mass: 8659.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.99 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 8, 2022 / Details: TITANIUM SILICATE FLAT MIRROR WITH PT
RadiationMonochromator: DOUBLE CRYSTAL / MULTILAYER MONOCHROMATOR SI(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.8.0352refinement
Cootmodel building
SCALAdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→25.3 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.1892 2573 5 %Random selection
Rwork0.1804 ---
obs-51451 96.93 %-
Displacement parametersBiso mean: 16.47 Å2
Refinement stepCycle: LAST / Resolution: 1.21→25.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 0 240 1778
LS refinement shellResolution: 1.21→1.23 Å
RfactorNum. reflection% reflection
Rfree0.228 --
Rwork0.204 --
obs-3384 92.8 %

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