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- PDB-7sa6: fHbp mutant 2416 bound to Fab JAR5 -

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Basic information

Entry
Database: PDB / ID: 7sa6
TitlefHbp mutant 2416 bound to Fab JAR5
Components
  • Factor H-binding protein 2416
  • JAR5 Heavy Chain
  • JAR5 Light Chain
KeywordsIMMUNE SYSTEM / antigen / PROTEIN BINDING
Biological speciesNeisseria meningitidis serogroup B (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChesterman, C. / Malito, E. / Bottomley, M.J.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Active Learning for Rapid Design: An iterative AI approach for accelerated vaccine design that combines active machine learning and high-throughput experimental evaluation
Authors: Chesterman, C. / Desautels, T. / Sierra, L.-J. / Arrildt, K. / Zemla, A. / Lau, E.Y. / Sundaram, S. / Laliberte, J. / Chen, L. / Ruby, A. / Mednikov, M. / Bertholet, S. / Yu, D. / Luisi, K. ...Authors: Chesterman, C. / Desautels, T. / Sierra, L.-J. / Arrildt, K. / Zemla, A. / Lau, E.Y. / Sundaram, S. / Laliberte, J. / Chen, L. / Ruby, A. / Mednikov, M. / Bertholet, S. / Yu, D. / Luisi, K. / Malito, E. / Mallett, C. / Bottomley, M.J. / Berg, R. / Faissol, D.
History
DepositionSep 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Factor H-binding protein 2416
H: JAR5 Heavy Chain
L: JAR5 Light Chain


Theoretical massNumber of molelcules
Total (without water)81,0123
Polymers81,0123
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-25 kcal/mol
Surface area28240 Å2
Unit cell
Length a, b, c (Å)148.990, 66.360, 105.370
Angle α, β, γ (deg.)90.000, 93.429, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Factor H-binding protein 2416


Mass: 29637.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Gene: fHbp / Production host: Escherichia coli (E. coli)
#2: Antibody JAR5 Heavy Chain


Mass: 27509.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody JAR5 Light Chain


Mass: 23865.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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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: 3.21 Å3/Da / Density % sol: 61.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Citrate pH 5 15% w/v PEG 4000 0.1 M Magnesium Chloride

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Data collection

DiffractionMean temperature: 170 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→19.93 Å / Num. obs: 22479 / % possible obs: 97.46 % / Redundancy: 9.15 % / CC1/2: 0.993 / Rmerge(I) obs: 0.1362 / Net I/σ(I): 9.15
Reflection shellResolution: 2.9→3.003 Å / Rmerge(I) obs: 1.366 / Num. unique obs: 2240 / CC1/2: 0.486

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5t5f

5t5f


Resolution: 2.9→19.93 Å / SU ML: 0.554 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.5744
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2899 2151 4.96 %
Rwork0.2486 41177 -
obs0.2507 22465 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4158 0 0 0 4158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314244
X-RAY DIFFRACTIONf_angle_d0.64065814
X-RAY DIFFRACTIONf_chiral_restr0.0458682
X-RAY DIFFRACTIONf_plane_restr0.0049761
X-RAY DIFFRACTIONf_dihedral_angle_d16.30791322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.44121240.36162776X-RAY DIFFRACTION98.51
2.97-3.040.43141510.34892763X-RAY DIFFRACTION98.28
3.04-3.120.37021490.34092799X-RAY DIFFRACTION98.56
3.12-3.210.39611450.32212724X-RAY DIFFRACTION98.25
3.22-3.320.38531490.32342829X-RAY DIFFRACTION98.22
3.32-3.440.33651350.31132730X-RAY DIFFRACTION97.48
3.44-3.570.3581450.29022711X-RAY DIFFRACTION96.68
3.57-3.730.35181390.28072474X-RAY DIFFRACTION88.82
3.73-3.930.30661440.27282682X-RAY DIFFRACTION94.23
3.93-4.170.26081330.23092827X-RAY DIFFRACTION99.56
4.17-4.490.25521480.20312780X-RAY DIFFRACTION99.19
4.49-4.940.26991480.19352785X-RAY DIFFRACTION99.15
4.94-5.640.24421510.21832799X-RAY DIFFRACTION98.83
5.64-7.050.33421400.24962746X-RAY DIFFRACTION97.53
7.05-19.930.20021500.21852752X-RAY DIFFRACTION97.12

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