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- PDB-2ncj: Solution Structure of the PriC DNA replication restart protein -

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Basic information

Entry
Database: PDB / ID: 2ncj
TitleSolution Structure of the PriC DNA replication restart protein
ComponentsUncharacterized protein
KeywordsDNA BINDING PROTEIN / DNA replication restart
Function / homologyPrimosomal replication PriB/PriC / PriB/PriC superfamily / Primosomal replication protein priC / Uncharacterized protein
Function and homology information
Biological speciesCronobacter sakazakii ATCC BAA-894 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsCornilescu, C.C. / Cornilescu, G. / Wessel, S.R. / Keck, J.L. / Markley, J.L.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structure and Function of the PriC DNA Replication Restart Protein.
Authors: Wessel, S.R. / Cornilescu, C.C. / Cornilescu, G. / Metz, A. / Leroux, M. / Hu, K. / Sandler, S.J. / Markley, J.L. / Keck, J.L.
History
DepositionApr 7, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: 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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)19,7331
Polymers19,7331
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 19733.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cronobacter sakazakii ATCC BAA-894 (bacteria)
Strain: ATCC BAA-894 / Gene: ESA_02803 / Production host: Escherichia coli (E. coli) / References: UniProt: A7MJV9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D C(CO)NH
1613D H(CCO)NH
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY aliphatic
11113D 1H-13C NOESY aromatic
1121(HB)CB(CGCD)HD
1131(HB)CB(CGCDCE)HE
11412D 1H-13C HSQC aliphatic
11512D ARTSY
11613D HCA(CO)N

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Sample preparation

DetailsContents: 0.4-0.6 mM [U-13C; U-15N] PriC, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O
SampleUnits: mM / Component: PriC-1 / Isotopic labeling: [U-13C; U-15N] / Conc. range: 0.4-0.6
Sample conditionsIonic strength: 20 / pH: 6.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA8004
Bruker AvanceBrukerAVANCE7505
Varian INOVAVarianINOVA9006

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettpeak picking
PIPPGarrettdata analysis
PIPPGarrettchemical shift assignment
TALOSCornilescu, Delaglio and Baxdihedral angle prediction
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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