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- PDB-8svj: Ubiquitin variant i53: mutant VHH with 53BP1 Tudor domain -

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Basic information

Entry
Database: PDB / ID: 8svj
TitleUbiquitin variant i53: mutant VHH with 53BP1 Tudor domain
Components
  • Tumor protein p53 binding protein 1
  • Ubiquitin varient i53 mutant VHH
KeywordsPROTEIN 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
: / BRCA1 C Terminus (BRCT) domain / Tumour suppressor p53-binding protein-1 Tudor domain / Tumour suppressor p53-binding protein-1 Tudor / : / : / 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: 1.5 Å
AuthorsHolden, J. / Partridge, J.R. / Wibowo, A.S. / Mulichak, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
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 varient i53 mutant VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7293
Polymers22,6372
Non-polymers921
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-8 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.98, 46.92, 90.57
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: Antibody Ubiquitin varient i53 mutant VHH


Mass: 8720.042 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.88 Å3/Da / Density % sol: 34.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, 0.2 M Trimethylamine N-oxide dehydrate, 13% w/v PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97939 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.5→22.71 Å / Num. obs: 27947 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 25.35 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.02361 / Net I/σ(I): 15.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.52 / Num. unique obs: 2730 / CC1/2: 0.879 / Rpim(I) all: 0.2826 / % possible all: 99.74

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
Cootmodel building
SCALAdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→22.71 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2195 1416 5.1 %
Rwork0.2096 --
obs-27947 99.76 %
Displacement parametersBiso mean: 32.92 Å2
Refinement stepCycle: LAST / Resolution: 1.5→22.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1560 0 6 111 1677
LS refinement shellResolution: 1.5→1.539 Å
RfactorNum. reflection% reflection
Rfree0.329 97 -
Rwork0.3 --
obs-2001 99.75 %

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