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- PDB-6xzw: Crystal structure of the meningococcal vaccine antigen fHbp in co... -

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Basic information

Entry
Database: PDB / ID: 6xzw
TitleCrystal structure of the meningococcal vaccine antigen fHbp in complex with a cross-reactive human Fab.
Components
  • Fab 4B3 (heavy chain)
  • Fab 4B3 (light chain)
  • Lipoprot_C domain-containing protein
KeywordsIMMUNE SYSTEM / Antigen-antibody complex / epitope mapping / lipoprotein / neisseria meningitidis
Function / homology
Function and homology information


bacterial extracellular vesicle / cell outer membrane
Similarity search - Function
: / : / Factor H binding protein, N-terminal / Factor H binding protein, C-terminal / Factor H binding protein, C-terminal / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Factor H binding protein
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVeggi, D. / Cozzi, R.
CitationJournal: Plos Pathog. / Year: 2020
Title: 4CMenB vaccine induces elite cross-protective human antibodies that compete with human factor H for binding to meningococcal fHbp.
Authors: Veggi, D. / Bianchi, F. / Santini, L. / Lo Surdo, P. / Chesterman, C.C. / Pansegrau, W. / Bechi, N. / Huang, Y. / Masignani, V. / Pizza, M. / Rappuoli, R. / Bottomley, M.J. / Cozzi, R. / Maione, D.
History
DepositionFeb 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Lipoprot_C domain-containing protein
L: Fab 4B3 (light chain)
H: Fab 4B3 (heavy chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5126
Polymers74,3263
Non-polymers1863
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-19 kcal/mol
Surface area29760 Å2
Unit cell
Length a, b, c (Å)47.340, 90.400, 97.940
Angle α, β, γ (deg.)90.000, 98.819, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Lipoprot_C domain-containing protein


Mass: 26896.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (strain MC58) (bacteria)
Gene: NMB1870 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9JXV4
#2: Antibody Fab 4B3 (light chain)


Mass: 23787.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Fab 4B3 (heavy chain)


Mass: 23642.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES, 20% w/v jeff ED-2001, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.4→46.78 Å / Num. obs: 29802 / % possible obs: 93 % / Redundancy: 3.4 % / Biso Wilson estimate: 50.17 Å2 / CC1/2: 0.99 / Net I/σ(I): 16.5
Reflection shellResolution: 2.4→2.48 Å / Num. unique obs: 3202 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PHENIX1.10_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KVD, 5TLK

3kvd

5tlk


Resolution: 2.4→46.78 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.48
RfactorNum. reflection% reflection
Rfree0.25 1444 4.84 %
Rwork0.2 --
obs0.2 29789 92.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 55.68 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5049 0 12 56 5117
Refine LS restraintsType: f_chiral_restr / Dev ideal: 0.0735652181087 / Number: 779
LS refinement shellResolution: 2.4→2.48 Å
RfactorNum. reflection% reflection
Rfree0.29 169 -
Rwork0.24 3032 -
obs--99.78 %

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