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- PDB-8bk2: X-ray structure of meningococcal factor H binding protein variant... -

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Basic information

Entry
Database: PDB / ID: 8bk2
TitleX-ray structure of meningococcal factor H binding protein variant 2 in complex with a specific and bactericidal human monoclonal antibody 1B1
Components
  • Fab Heavy chainFragment antigen-binding
  • Fab light Chains
  • Factor H-binding protein
KeywordsPROTEIN BINDING / Meningococcus / Antigen / Human Monoclonal / fHbp / Bactericidal / Factor H displacement / Vaccine.
Function / homologyFactor H binding protein, C-terminal / Factor H binding protein, C-terminal / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / IMIDAZOLE / Factor H-binding protein
Function and homology information
Biological speciesNeisseria meningitidis serogroup B (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsVeggi, D. / Bottomley, J.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Bactericidal human monoclonal antibody 1B1 specific for meningococcal factor H binding protein variant 2 and displaces human factor H
Authors: Veggi, D. / Bottomley, J.M.
History
DepositionNov 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Factor H-binding protein
B: Factor H-binding protein
C: Factor H-binding protein
H: Fab Heavy chain
L: Fab light Chains
D: Fab Heavy chain
E: Fab light Chains
F: Fab Heavy chain
G: Fab light Chains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,07120
Polymers226,8079
Non-polymers1,26411
Water3,837213
1
A: Factor H-binding protein
H: Fab Heavy chain
L: Fab light Chains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1096
Polymers75,6023
Non-polymers5073
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Factor H-binding protein
D: Fab Heavy chain
E: Fab light Chains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9208
Polymers75,6023
Non-polymers3175
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Factor H-binding protein
F: Fab Heavy chain
G: Fab light Chains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0436
Polymers75,6023
Non-polymers4403
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.153, 135.641, 121.530
Angle α, β, γ (deg.)90.000, 105.180, 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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Protein , 1 types, 3 molecules ABC

#1: Protein Factor H-binding protein


Mass: 28217.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Gene: fhbp / Production host: Escherichia coli (E. coli) / References: UniProt: B9VX96

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Antibody , 2 types, 6 molecules HDFLEG

#2: Antibody Fab Heavy chain / Fragment antigen-binding


Mass: 23871.760 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Fab light Chains


Mass: 23513.143 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 7 types, 224 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#7: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#8: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#9: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.09M Sodium Nitrate, Sodium Phosphate dibasic, Ammonium Solphate, 0.1 M Buffer Imidazole, MES monohydrate, pH6.5 and as precipitant mix 25% v/v MPD, 25% PEG 100, 25% w/v PEG 3350.

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Data collection

DiffractionMean temperature: 150 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 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: 2.41→49.66 Å / Num. obs: 92813 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 62.03 Å2 / CC1/2: 0.997 / Net I/σ(I): 10
Reflection shellResolution: 2.41→2.49 Å / Num. unique obs: 9128 / CC1/2: 0.494

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XZW

6xzw


Resolution: 2.41→49.66 Å / SU ML: 0.4322 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.5397
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2696 4732 5.11 %
Rwork0.2044 87913 -
obs0.2076 92645 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.98 Å2
Refinement stepCycle: LAST / Resolution: 2.41→49.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13487 0 83 213 13783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007913841
X-RAY DIFFRACTIONf_angle_d0.989418747
X-RAY DIFFRACTIONf_chiral_restr0.05582114
X-RAY DIFFRACTIONf_plane_restr0.00762417
X-RAY DIFFRACTIONf_dihedral_angle_d16.51084915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.440.41461560.36772873X-RAY DIFFRACTION98.12
2.44-2.470.43861320.36122942X-RAY DIFFRACTION98.65
2.47-2.50.43281650.33862911X-RAY DIFFRACTION99.58
2.5-2.530.39661770.33692885X-RAY DIFFRACTION99.64
2.53-2.560.44941540.31582943X-RAY DIFFRACTION99.65
2.56-2.60.36891730.30912865X-RAY DIFFRACTION99.9
2.6-2.630.34651730.29022925X-RAY DIFFRACTION99.97
2.63-2.670.35241560.2742938X-RAY DIFFRACTION99.84
2.67-2.710.34641650.28022929X-RAY DIFFRACTION99.87
2.71-2.760.34671470.28272949X-RAY DIFFRACTION99.81
2.76-2.810.34421670.28852891X-RAY DIFFRACTION99.87
2.81-2.860.34591550.29172981X-RAY DIFFRACTION99.9
2.86-2.910.33591510.26512882X-RAY DIFFRACTION99.87
2.91-2.970.39851480.27712991X-RAY DIFFRACTION99.87
2.97-3.040.33261640.25952890X-RAY DIFFRACTION99.9
3.04-3.110.30581530.24782929X-RAY DIFFRACTION99.81
3.11-3.180.30911870.23072929X-RAY DIFFRACTION99.74
3.18-3.270.26161630.22352925X-RAY DIFFRACTION99.97
3.27-3.370.32271660.23562932X-RAY DIFFRACTION99.71
3.37-3.480.3471510.22852947X-RAY DIFFRACTION99.87
3.48-3.60.23911390.21432932X-RAY DIFFRACTION99.87
3.6-3.740.28011560.20312947X-RAY DIFFRACTION99.87
3.74-3.910.27791570.18512937X-RAY DIFFRACTION99.84
3.91-4.120.24031580.1752951X-RAY DIFFRACTION99.71
4.12-4.380.20431540.15972937X-RAY DIFFRACTION99.39
4.38-4.720.22761510.14532940X-RAY DIFFRACTION99.26
4.72-5.190.21281730.1592910X-RAY DIFFRACTION99.23
5.19-5.940.24211380.1722951X-RAY DIFFRACTION98.56
5.94-7.480.22521530.19192945X-RAY DIFFRACTION98.95
7.48-49.660.20381500.16453006X-RAY DIFFRACTION99.15

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