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- PDB-6y54: Crystal structure of a Neisseria meningitidis serogroup A capsula... -

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Basic information

Entry
Database: PDB / ID: 6y54
TitleCrystal structure of a Neisseria meningitidis serogroup A capsular oligosaccharide bound to a functional Fab
Components
  • Fab A1.1 H chain
  • Fab A1.1 L chain
KeywordsIMMUNE SYSTEM / antigen-antibody complex / epitope mapping / carbohydrate / glycan
Function / homologyIODIDE ION / Chem-OA8 / Chem-OAB / Chem-OOW
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsDello Iacono, L. / Henriques, P. / Adamo, R.
Funding support Italy, 1items
OrganizationGrant numberCountry
European Commission675671 Italy
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structure of a protective epitope reveals the importance of acetylation of Neisseria meningitidis serogroup A capsular polysaccharide.
Authors: Henriques, P. / Dello Iacono, L. / Gimeno, A. / Biolchi, A. / Romano, M.R. / Arda, A. / Bernardes, G.J.L. / Jimenez-Barbero, J. / Berti, F. / Rappuoli, R. / Adamo, R.
History
DepositionFeb 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
H: Fab A1.1 H chain
L: Fab A1.1 L chain
M: Fab A1.1 H chain
N: Fab A1.1 L chain
O: Fab A1.1 H chain
P: Fab A1.1 L chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,89627
Polymers146,2396
Non-polymers4,65721
Water46826
1
H: Fab A1.1 H chain
L: Fab A1.1 L chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,48811
Polymers48,7462
Non-polymers1,7419
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: Fab A1.1 H chain
N: Fab A1.1 L chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,55311
Polymers48,7462
Non-polymers1,8069
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
O: Fab A1.1 H chain
P: Fab A1.1 L chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8565
Polymers48,7462
Non-polymers1,1103
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.609, 153.205, 101.051
Angle α, β, γ (deg.)90.000, 91.527, 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

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Antibody , 2 types, 6 molecules HMOLNP

#1: Antibody Fab A1.1 H chain


Mass: 24520.445 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Fab A1.1 L chain


Mass: 24225.871 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Non-polymers , 6 types, 47 molecules

#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-OOW / {[(2R,3S,4R,5S,6R)-5-acetamido-3-hydroxy-4-(2-oxopropyl)-6-(phosphonooxy)oxan-2-yl]methoxy}phosphonic acid


Mass: 423.204 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H19NO13P2
#6: Chemical ChemComp-OA8 / {[(2R,3S,4R,5S,6S)-3-(acetyloxy)-5-acetamido-4,6-dihydroxyoxan-2-yl]methoxy}phosphonic acid


Mass: 343.224 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H18NO10P
#7: Chemical ChemComp-OAB / {[(2R,3S,4R,5S,6S)-5-acetamido-3,6-dihydroxy-4-(2-oxopropyl)oxan-2-yl]methoxy}phosphonic acid


Mass: 343.224 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H18NO10P
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES pH 5.4, 255 mM KI 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.67→49.74 Å / Num. obs: 44254 / % possible obs: 97.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 44.08 Å2 / CC1/2: 0.979 / Net I/σ(I): 6.4
Reflection shellResolution: 2.67→2.76 Å / Num. unique obs: 4231 / CC1/2: 0.598

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KVF, 3FO9

5kvf

3fo9


Resolution: 2.67→49.74 Å / SU ML: 0.4614 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.4224
RfactorNum. reflection% reflection
Rfree0.2672 2185 4.96 %
Rwork0.2102 --
obs0.213 44059 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.93 Å2
Refinement stepCycle: LAST / Resolution: 2.67→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8219 0 225 26 8470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00858642
X-RAY DIFFRACTIONf_angle_d1.14911778
X-RAY DIFFRACTIONf_chiral_restr0.20831334
X-RAY DIFFRACTIONf_plane_restr0.00821466
X-RAY DIFFRACTIONf_dihedral_angle_d18.75183036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.730.40451390.392403X-RAY DIFFRACTION89.79
2.73-2.790.38991200.31592650X-RAY DIFFRACTION98.19
2.79-2.860.34021530.28682619X-RAY DIFFRACTION98.58
2.86-2.940.38861340.2822667X-RAY DIFFRACTION98.49
2.94-3.030.31051360.25682632X-RAY DIFFRACTION98.93
3.03-3.120.30811470.24092669X-RAY DIFFRACTION98.43
3.12-3.230.31521480.24072609X-RAY DIFFRACTION98.53
3.23-3.360.30861330.242688X-RAY DIFFRACTION99.37
3.36-3.520.3241060.25782535X-RAY DIFFRACTION91.99
3.52-3.70.29351520.22932507X-RAY DIFFRACTION94.9
3.7-3.930.29421130.21842506X-RAY DIFFRACTION92.84
3.93-4.240.25511510.17192639X-RAY DIFFRACTION98.66
4.24-4.660.17511260.13872671X-RAY DIFFRACTION98.49
4.66-5.340.17141530.13732686X-RAY DIFFRACTION99.16
5.34-6.720.21371470.17872678X-RAY DIFFRACTION99.02
6.72-49.740.23851270.19252715X-RAY DIFFRACTION98.34

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