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- PDB-2le2: Novel dimeric structure of phage phi29-encoded protein p56: Insig... -

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Basic information

Entry
Database: PDB / ID: 2le2
TitleNovel dimeric structure of phage phi29-encoded protein p56: Insights into Uracil-DNA glycosylase inhibition
ComponentsP56
KeywordsHYDROLASE INHIBITOR / DNA repair inhibition / UDG inhibition / DNA mimicry
Function / homology: / Phage phi29, UDG inhibitor P56 / Double Stranded RNA Binding Domain - #30 / Double Stranded RNA Binding Domain / biological process involved in interaction with host / Other non-globular / Special / Protein p56
Function and homology information
Biological speciesBacillus phage phi29 (virus)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsAsensio, J. / Perez-Lago, L. / Lazaro, J.M. / Gonzalez, C. / Serrano-Heras, G. / Salas, M.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Novel dimeric structure of phage 29-encoded protein p56: insights into uracil-DNA glycosylase inhibition.
Authors: Asensio, J.L. / Perez-Lago, L. / Lazaro, J.M. / Gonzalez, C. / Serrano-Heras, G. / Salas, M.
History
DepositionJun 6, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Structure summary
Revision 1.2Dec 28, 2011Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P56
B: P56


Theoretical massNumber of molelcules
Total (without water)13,1432
Polymers13,1432
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein P56


Mass: 6571.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Gene: 0.8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q38503

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of Uracil-DNA glycosylase inhibitor p56 from phage phi-29
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D 1H-1H COSY
1432D 1H-1H NOESY
1522D 1H-15N HSQC
1623D HN(CA)CB
1723D CBCA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM p56, 100 mM sodium chloride, 10 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-98% 13C; U-98% 15N] p56, 100 mM sodium chloride, 10 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM p56, 100 mM sodium chloride, 10 mM sodium phosphate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMp56-11
100 mMsodium chloride-21
10 mMpotassium phosphate-31
0.5 mMp56-4[U-98% 13C; U-98% 15N]2
100 mMsodium chloride-52
10 mMpotassium phosphate-62
0.5 mMp56-73
100 mMsodium chloride-83
10 mMpotassium phosphate-93
Sample conditionsIonic strength: 0.13 / pH: 5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameDeveloperClassification
XEASYBartels et al.data analysis
DYANAGuntert, Braun and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 20

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