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- PDB-2nba: Solution NMR structure of the minor DNA-uptake pilin ComP from Ne... -

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Basic information

Entry
Database: PDB / ID: 2nba
TitleSolution NMR structure of the minor DNA-uptake pilin ComP from Neisseri subflava
ComponentsPrepilin-type cleavage/methylation N-terminal domain protein
KeywordsDNA BINDING PROTEIN / Type Iv pilin / DNA-binding / DNA transformation / Neisseriaceae
Function / homologyType IV pilus non-core minor pilin PilE-like / Type IV minor pilin ComP, DNA uptake sequence receptor / type IV pilus assembly / Prokaryotic N-terminal methylation site / membrane => GO:0016020 / Prepilin-type cleavage/methylation N-terminal domain protein
Function and homology information
Biological speciesNeisseria subflava NJ9703 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBerry, J.L. / Xu, Y.
CitationJournal: Structure / Year: 2016
Title: A Comparative Structure/Function Analysis of Two Type IV Pilin DNA Receptors Defines a Novel Mode of DNA Binding.
Authors: Berry, J.L. / Xu, Y. / Ward, P.N. / Lea, S.M. / Matthews, S.J. / Pelicic, V.
History
DepositionFeb 2, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 29, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prepilin-type cleavage/methylation N-terminal domain protein


Theoretical massNumber of molelcules
Total (without water)13,0711
Polymers13,0711
Non-polymers00
Water0
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 Prepilin-type cleavage/methylation N-terminal domain protein


Mass: 13071.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria subflava NJ9703 (bacteria) / Gene: NEISUBOT_04550 / Plasmid: pET 28(b) / Production host: Escherichia coli (E. coli) / References: UniProt: D3A5N9

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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 HN(CA)CB
1313D HNCO
1413D CBCA(CO)NH
1513D 1H-15N NOESY
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D 1H-13C NOESY aliphatic

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Sample preparation

DetailsContents: 750 uM [U-98% 13C; U-98% 15N] ComP, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 750 uM / Component: ComP-1 / Isotopic labeling: [U-98% 13C; U-98% 15N]
Sample conditionsIonic strength: 0.05 / pH: 6 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.1Linge, O'Donoghue and Nilgesstructure solution
ARIA2.1Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3052 / NOE intraresidue total count: 744 / NOE long range total count: 555 / NOE medium range total count: 273 / NOE sequential total count: 445
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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