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- PDB-8acz: Solid-State NMR Atomic-Resolution Structure of the Protein Encode... -

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Basic information

Entry
Database: PDB / ID: 8acz
TitleSolid-State NMR Atomic-Resolution Structure of the Protein Encoded by Gene V of fd Bacteriophage in Complex with Viral ssDNA
ComponentsDNA-Binding protein G5P
KeywordsDNA BINDING PROTEIN / nucleoprotein complex / ssDNA binding
Function / homologyBacteriophage M13, G5P, DNA-binding / Helix-destabilising protein / rolling circle single-stranded viral DNA replication / single-stranded DNA binding / DNA replication / Nucleic acid-binding, OB-fold / DNA-Binding protein G5P
Function and homology information
Biological speciesInoviridae (virus)
MethodSOLID-STATE NMR / simulated annealing
AuthorsShamir, Y. / Goldbourt, A.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation847/17 Israel
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Atomic-Resolution Structure of the Protein Encoded by Gene V of fd Bacteriophage in Complex with Viral ssDNA Determined by Magic-Angle Spinning Solid-State NMR.
Authors: Shamir, Y. / Goldbourt, A.
History
DepositionJul 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 19, 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: DNA-Binding protein G5P


Theoretical massNumber of molelcules
Total (without water)11,0971
Polymers11,0971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, The binding ratio of 4 nucleotides per monomer used for sample preparation of the nucleoprotein complex was verified via gel electrophoresis.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein DNA-Binding protein G5P / G5P / Single-stranded DNA-binding protein


Mass: 11096.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: isotopically labeled gVp in complex with natural abundance viral ssDNA of fd bacteriophage
Source: (gene. exp.) Inoviridae (virus) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P69544

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D DARR15ms
121isotropic12D DARR100ms
132isotropic12D DARR50ms
142isotropic12D DARR100ms
152isotropic12D DARR150ms
182isotropic12D CORD150ms
172isotropic12D DARR300ms
162isotropic12D CORD300ms
192isotropic12D DARR300ms #2
1102isotropic12D CHHC150u
1112isotropic12D CHHC300u
1121isotropic12D DARR5ms
1131isotropic12D DARR250ms
1141isotropic12D RFDR6
1151isotropic12D INADEQUATE
1161isotropic13D NCOCX25
1171isotropic13D NCACX25
1182isotropic12D DARR5ms
1192isotropic12D DARR15ms
1202isotropic12D NCA
1212isotropic12D NCO
1222isotropic13D NCOCX100
1232isotropic13D NCACX100

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solid1200 g/L [U-100% 13C; U-100% 15N] gVp of fd bacteriophage in complex with the viral ssDNA, 22 g/L ssDNA of fd phage, 200mM NaCl, 1mM EDTA and 10mM Tris-HClU-13C/15N gVp in complex with fd ssDNA200mM NaCl, 1mM EDTA and 10mM Tris-HCl
solid2200 g/L [1,3-13C]-glycerol gVp of fd bacteriophage in complex with the viral ssDNA, 22 g/L ssDNA of fd phage, 200mM NaCl, 1mM EDTA and 10mM Tris-HCl[1,3-13C]-glycerol-labeled gVp in complex with fd ssDNA200mM NaCl, 1mM EDTA and 10mM Tris-HCl
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 g/LgVp of fd bacteriophage in complex with the viral ssDNA[U-100% 13C; U-100% 15N]1
22 g/LssDNA of fd phagenatural abundance1
200 g/LgVp of fd bacteriophage in complex with the viral ssDNA[1,3-13C]-glycerol2
22 g/LssDNA of fd phagenatural abundance2
Sample conditionsIonic strength: 200mM NaCl mM / Label: gvp_sample_conditions / pH: 7.4 / Pressure: 1 atm / Temperature: 263 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRFAM-SPARKY1.47Lee W, Tonelli M, Markley JL.chemical shift assignment
NMRFAM-SPARKY1.47Lee W, Tonelli M, Markley JL.peak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

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