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- PDB-2kc0: Solution structure of the factor H binding protein -

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Basic information

Entry
Database: PDB / ID: 2kc0
TitleSolution structure of the factor H binding protein
Componentslipoprotein
KeywordsPROTEIN BINDING / solution structure / Neisseria meningitidis / antigen / fHbp / Lipoprotein
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Immunoglobulin-like - #1980 / : / : / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Immunoglobulin-like - #1980 / : / : / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Factor H-binding protein / Factor H binding protein variant B24
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailsfewest violations, model 1
AuthorsCantini, F. / Veggi, D. / Dragonetti, S. / Savino, S. / Scarselli, M. / Romagnoli, G. / Pizza, M. / Banci, L. / Rappuoli, R.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Solution Structure of the Factor H-binding Protein, a Survival Factor and Protective Antigen of Neisseria meningitidis
Authors: Cantini, F. / Veggi, D. / Dragonetti, S. / Savino, S. / Scarselli, M. / Romagnoli, G. / Pizza, M. / Banci, L. / Rappuoli, R.
History
DepositionDec 13, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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)27,4581
Polymers27,4581
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)25 / 900target function
RepresentativeModel #1fewest violations

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Components

#1: Protein lipoprotein / / Factor H binding protein variant B24_002


Mass: 27457.666 Da / Num. of mol.: 1 / Fragment: UNP residues 8-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: nmb1870 / Plasmid: pET20b+ / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: Q6VRZ6, UniProt: Q6QCC2*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Factor H binding protein is a 27 kDa lipoprotein of Neisseria meningitidis discovered while screening the bacterial genome for vaccine candidates. The protein is composed of two independent ...Details: Factor H binding protein is a 27 kDa lipoprotein of Neisseria meningitidis discovered while screening the bacterial genome for vaccine candidates. The protein is composed of two independent barrels connected by a short link
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1332D 1H-1H NOESY
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HNCA
1713D HNCO
1823D (H)CCH-TOCSY
1923D 1H-15N NOESY
11023D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4mM [U-100% 13C; U-100% 15N; U-80% 2H] lipoprotein, 50mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
20.5mM [U-98% 13C; U-98% 15N] lipoprotein, 50mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
30.8mM lipoprotein, 50mM potassium phosphate-6, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMlipoprotein[U-100% 13C; U-100% 15N; U-80% 2H]1
0.5 mMlipoprotein[U-98% 13C; U-98% 15N]2
0.8 mMlipoprotein3
Sample conditionsIonic strength: 50mM phosphate buffer / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CARAKeller and Wuthrichchemical shift assignment
XEASYBartels et al.data analysis
ProcheckNMR10Laskowski and MacArthurvalidation
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: The structures were based on a total of 2987 meaningful distance constraints, 316 dihedral angle restraints and 73 RDCs, 900 random conformers were annealed in 13000 steps
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 900 / Conformers submitted total number: 25 / Representative conformer: 1

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