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- PDB-2n59: Solution Structure of R. palustris CsgH -

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Basic information

Entry
Database: PDB / ID: 2n59
TitleSolution Structure of R. palustris CsgH
ComponentsPutative uncharacterized protein CsgH
KeywordsUNKNOWN FUNCTION
Function / homologyUncharacterized protein
Function and homology information
Biological speciesRhodopseudomonas palustris DX-1 (phototrophic)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsHawthorne, W.J. / Taylor, J.D. / Escalera-Maurer, A. / Lambert, S. / Koch, M. / Scull, N. / Sefer, L. / Xu, Y. / Matthews, S.J.
CitationJournal: Sci Rep / Year: 2016
Title: Electrostatically-guided inhibition of Curli amyloid nucleation by the CsgC-like family of chaperones.
Authors: Taylor, J.D. / Hawthorne, W.J. / Lo, J. / Dear, A. / Jain, N. / Meisl, G. / Andreasen, M. / Fletcher, C. / Koch, M. / Darvill, N. / Scull, N. / Escalera-Maurer, A. / Sefer, L. / Wenman, R. / Lambert, S. / Jean, J. / Xu, Y. / Turner, B. / Kazarian, S.G. / Chapman, M.R. / Bubeck, D. / de Simone, A. / Knowles, T.P. / Matthews, S.J.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 13, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein CsgH


Theoretical massNumber of molelcules
Total (without water)11,1841
Polymers11,1841
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Putative uncharacterized protein CsgH


Mass: 11183.521 Da / Num. of mol.: 1 / Fragment: UNP residues 10-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris DX-1 (phototrophic)
Strain: DX-1 / Gene: csgH, Rpdx1_1250 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express / References: UniProt: E6VF87

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment

Conditions-ID: 1

Experiment-IDSolution-IDType
112D 1H-15N HSQC
213D HN(CA)CB
313D CBCA(CO)NH
413D HNCO
513D HN(CA)CO
613D HBHA(CO)NH
713D CC(CO)NH
813D (H)CCH-TOCSY
922D 1H-13C HSQC aromatic
1022D 1H-1H NOESY
1123D 1H-13C NOESY
1213D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1400 uM [U-98% 13C; U-98% 15N] CsgH, 150 mM sodium chloride, 10 mM MES, 10 % [U-2H] D2O, 90% H2O/10% D2O90% H2O/10% D2O
2400 uM [U-98% 13C; U-98% 15N] CsgH, 150 mM sodium chloride, 10 mM MES, 100 % [U-2H] D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMCsgH-1[U-98% 13C; U-98% 15N]1
150 mMsodium chloride-21
10 mMMES-31
10 %D2O-4[U-2H]1
400 uMCsgH-5[U-98% 13C; U-98% 15N]2
150 mMsodium chloride-62
10 mMMES-72
100 %D2O-8[U-2H]2
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: ambient / Temperature: 292 K

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NMR measurement

NMR spectrometer

Manufacturer: Bruker / Model: Avance / Type: Bruker Avance

Field strength (MHz)Spectrometer-ID
6001
8002
9503

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
NMRView5.2.2Johnson, One Moon Scientificchemical shift assignment
CcpNmr2.4.0Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED.chemical shift assignment
CcpNmr2.4.0Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED.peak picking
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIArefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1721 / NOE intraresidue total count: 575 / NOE long range total count: 373 / NOE medium range total count: 54 / NOE sequential total count: 200 / Disulfide bond constraints total count: 1 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 85 / Protein psi angle constraints total count: 85
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20 / Representative conformer: 1

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