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- PDB-1ys5: Solution structure of the antigenic domain of GNA1870 of Neisseri... -

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Basic information

Entry
Database: PDB / ID: 1ys5
TitleSolution structure of the antigenic domain of GNA1870 of Neisseria meningitidis
Componentslipoprotein
KeywordsSIGNALING PROTEIN / vaccine candidate / Neisseria meningitidis / beta-barrel structure
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
: / : / Factor H binding protein, N-terminal / Factor H binding protein, C-terminal / Factor H binding protein, C-terminal / Porin - #90 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / Factor H binding protein variant B24
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsCantini, F. / Savino, S. / Masignani, V. / Pizza, M. / Scarselli, M. / Swennen, E. / Romagnoli, G. / Veggi, D. / Banci, L. / Rappuoli, R.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Solution structure of the immunodominant domain of protective antigen GNA1870 of Neisseria meningitidis
Authors: Cantini, F. / Savino, S. / Scarselli, M. / Masignani, V. / Pizza, M. / Romagnoli, G. / Swennen, E. / Veggi, D. / Banci, L. / Rappuoli, R.
History
DepositionFeb 7, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lipoprotein


Theoretical massNumber of molelcules
Total (without water)17,6271
Polymers17,6271
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)30 / 400target function
RepresentativeModel #12closest to the average

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Components

#1: Protein lipoprotein /


Mass: 17626.607 Da / Num. of mol.: 1 / Fragment: immunodominant C-terminal BC domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: gna1870 / Plasmid: pET20b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 46562309, UniProt: Q6VRZ6*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
132HNHA
1423D 15N-separated NOESY
153CBCANH
163CBCA(CO)NH
173HNCO
183HN(CA)CO
193CCH-TOCSY
11033D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
14mM GNA1870; 20mM phosphate buffer90% H2O/10% D2O
21mM GNA1870 15N labelled; 20mM phosphate buffer;90% H2O/10% D2O
32mM GNA1870 15N and 13C labelled; 20mM phosphate buffer;90% H2O/10% D2O
Sample conditionsIonic strength: 20mM phosphate buffer / pH: 7 / Pressure: ambient / Temperature: 298 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
XwinNMRcollection
CARA1.2The Computer Aided Resonance Assignment Tutorial by Rochus Keller, first edition 2004data analysis
DYANA1.5G ntert et al, 1997structure solution
CANDID2Herrmann et al, 2002structure solution
Amber5Pearlman et al, 1987refinement
PROCHECK-NMR, AQUALaskowski et al, 1996data analysis
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: the structures were based on a total of 2242 meaningful distance constraints, 149 dihedral angle restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 30

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