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- PDB-2jr1: Solution structure of the DNA binding domain of a nucleoid-associ... -

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Basic information

Entry
Database: PDB / ID: 2jr1
TitleSolution structure of the DNA binding domain of a nucleoid-associated protein, H-NS, from the phytopathogen Xylella fastidiosa.
ComponentsVirulence regulator
KeywordsDNA BINDING PROTEIN / H-NS / DNA biding protein / Xylella fastidiosa
Function / homologyHistone-like nucleoid-structuring protein H-NS / Histone-like protein H-NS, C-terminal domain / H-NS histone C-terminal domain / Domain in histone-like proteins of HNS family / Double Stranded RNA Binding Domain / DNA binding / 2-Layer Sandwich / Alpha Beta / Virulence regulator
Function and homology information
Biological speciesXylella fastidiosa (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, minimization
AuthorsRosselli, L.K. / Sforca, M.L. / Souza, A.P. / Zeri, A.C.
CitationJournal: To be Published
Title: Solution structure of the DNA binding domain of a nucleoid-associated protein, H-NS, from the phytopathogen Xylella fastidiosa.
Authors: Rosselli, L.K. / Sforca, M.L. / Souza, A.P. / Zeri, A.C.
History
DepositionJun 18, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Virulence regulator


Theoretical massNumber of molelcules
Total (without water)8,8471
Polymers8,8471
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 / 40structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein Virulence regulator


Mass: 8847.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylella fastidiosa (bacteria) / Strain: 9a5c / Gene: XF0749 / Plasmid: pET32Xa/LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9PFC9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D CBCA(CO)NH
1323D (H)CCH-TOCSY
1423D CCH-TOCSY
1513D 1H-15N TOCSY
1613D 1H-15N NOESY
1713D 1H-15N NOESY
1823D 1H-13C NOESY
193Heteronuclear NOE
1103Heteronuclear NOE
1113T1 Relaxation
1123T1 Relaxation
1133T2 Relaxation
1143T2 Relaxation
NMR detailsText: H/D exchange Nhsqc experiments were performed using smaple_2, sample_condiction_2, and spectrometer_2

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-99% 13C; U-99% 15N] HNS79c, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-99% 13C; U-99% 15N] HNS79c, 100% D2O100% D2O
30.5 mM [U-99% 15N] HNS79c, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMprotein_HNS79c[U-99% 13C; U-99% 15N]1
0.5 mMprotein_HNS79c[U-99% 13C; U-99% 15N]2
0.5 mMprotein_HNS79c[U-99% 15N]3
Sample conditionsIonic strength: 0.25 / pH: 6.8 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe5Delaglio, F. et al.processing
NMRView5Johnson, B.A. et al.data analysis
DYANAGuntert, P. et al.structure solution
DiscoverAccelrysrefinement
RefinementMethod: torsion angle dynamics, minimization / Software ordinal: 1
Details: after the torsion angle dynamics with Dyana software, structures were minimized until 1 kcal/A in the discover module of the Insight package using conjugate gradients.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 40 / Conformers submitted total number: 20

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