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- PDB-2rt6: Backbone 1H, 13C, and 15N Chemical Shift Assignments for PriC N-t... -

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Basic information

Entry
Database: PDB / ID: 2rt6
TitleBackbone 1H, 13C, and 15N Chemical Shift Assignments for PriC N-terminal domain
ComponentsPrimosomal replication protein N''
KeywordsDNA BINDING PROTEIN / Primosome / Replication restart / PriC
Function / homology
Function and homology information


DnaB-DnaC-Rep-PriC complex / DnaB-DnaC-DnaT-PriA-PriC complex / primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / replication fork processing / DNA replication initiation / DNA-templated DNA replication / DNA binding
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #340 / Primosomal replication PriB/PriC / PriB/PriC superfamily / Primosomal replication protein priC / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Primosomal replication protein N''
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsAramaki, T. / Abe, Y. / Katayama, T. / Ueda, T.
CitationJournal: Protein Sci. / Year: 2013
Title: Solution structure of the N-terminal domain of a replication restart primosome factor, PriC, in Escherichia coli.
Authors: Aramaki, T. / Abe, Y. / Katayama, T. / Ueda, T.
History
DepositionApr 24, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references / Category: citation / database_2 / pdbx_nmr_software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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: Primosomal replication protein N''


Theoretical massNumber of molelcules
Total (without water)11,0081
Polymers11,0081
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Primosomal replication protein N''


Mass: 11007.533 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0467, JW0456, priC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23862

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1312D 1H-13C HSQC aliphatic
1412D 1H-13C HSQC aromatic
1513D CBCA(CO)NH
1613D C(CO)NH
1713D HNCO
1813D HNCA
1913D HN(CA)CB
11013D HBHA(CO)NH
11113D HN(CO)CA
11213D H(CCO)NH
11313D (H)CCH-TOCSY
11413D 1H-15N NOESY
11513D 1H-15N TOCSY
11613D 1H-13C NOESY aliphatic
11713D 1H-13C NOESY aromatic
11813D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-99% 13C; U-99% 15N] PriC N-terminal domain-1, 150 mM sodium chloride-2, 90% H2O/10% D2O90% H2O/10% D2O
20.2 mM [U-98% 15N] PriC N-terminal domain-3, 150 mM sodium chloride-4, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMPriC N-terminal domain-1[U-99% 13C; U-99% 15N]1
150 mMsodium chloride-21
0.2 mMPriC N-terminal domain-3[U-98% 15N]2
150 mMsodium chloride-42
Sample conditionsIonic strength: 150 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
Olivia1.16.6Olivia Developer Teamchemical shift assignment
Olivia1.16.6Olivia Developer Teamdata analysis
CNS1.21refinement
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 908 / NOE intraresidue total count: 297 / NOE long range total count: 124 / NOE medium range total count: 172 / NOE sequential total count: 307 / Hydrogen bond constraints total count: 0 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 87 / Protein psi angle constraints total count: 87
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 2.7 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.01 Å / Maximum torsion angle constraint violation: 4.06 ° / Maximum upper distance constraint violation: 0.2 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.0022 Å / Distance rms dev error: 0.0002 Å

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