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- PDB-6v1w: NMR Structure of C-terminal Domain of phi29 ATPase -

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Basic information

Entry
Database: PDB / ID: 6v1w
TitleNMR Structure of C-terminal Domain of phi29 ATPase
ComponentsDNA packaging protein
KeywordsVIRAL PROTEIN / viral packaging motor / terminase / RNase H fold
Function / homology
Function and homology information


viral DNA genome packaging / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding
Similarity search - Function
Podovirus DNA packaging protein / Podovirus DNA encapsidation protein (Gp16) / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA packaging protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodSOLUTION NMR / simulated annealing
AuthorsMahler, B. / Mao, H. / Morais, M.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM122979-02 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: NMR structure of a vestigial nuclease provides insight into the evolution of functional transitions in viral dsDNA packaging motors.
Authors: Mahler, B.P. / Bujalowski, P.J. / Mao, H. / Dill, E.A. / Jardine, P.J. / Choi, K.H. / Morais, M.C.
History
DepositionNov 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
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: DNA packaging protein


Theoretical massNumber of molelcules
Total (without water)14,1951
Polymers14,1951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, sedimentation velocity
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50Lowest total energy and zero NOE violations
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA packaging protein / ATPase gp16 / Gene product 16 / gp16 / Protein p16


Mass: 14195.173 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 223-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Gene: 16 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P11014, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 15N NOESY-HSQC
122isotropic13D 13C-edited NOESY-HSQC aliphatic
132isotropic13D 13C-editied NOESY-HSQC aromatic
142isotropic13D HSQC-NOESY-HSQC
151isotropic1HD-exchange
163isotropic23D HNCA
173isotropic23D HN(CA)CB
183isotropic33D CBCA(CO)NH
1123isotropic33D HNCO
191isotropic13D 1H-15N TOCSY
1102isotropic33D (H)CCH-TOCSY
1112isotropic13D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 uM [U-15N] protein, 50 mM MES, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution21 uM [U-13C] protein, 50 mM [U-2H] MES, 99.9% D2O13C_sample99.9% D2O
solution31 uM U-15N, U-13C protein, 50 mM MES, 90% H2O/10% D2ODL_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 uMprotein[U-15N]1
1 uMprotein[U-13C]2
1 uMproteinU-15N, U-13C3
50 mMMESnatural abundance1
50 mMMES[U-2H]2
50 mMMESnatural abundance3
Sample conditionsIonic strength: 0 mM / Label: condition_1 / pH: 6 / Pressure: 1013 mbar / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III7501TCI cryoprobe
Bruker AVANCE IIIBrukerAVANCE III6002QCI cryoprobe
Bruker AVANCE IIIBrukerAVANCE III8003TCI cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView9.2.0Johnson, One Moon Scientificdata analysis
TALOS-NCornilescu, Delaglio and Baxchemical shift calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Lowest total energy and zero NOE violations
Conformers calculated total number: 50 / Conformers submitted total number: 15

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