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- PDB-7sbz: JAR5 Fab bound to fHbp v1.1 crystallized in space group I422 -

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Basic information

Entry
Database: PDB / ID: 7sbz
TitleJAR5 Fab bound to fHbp v1.1 crystallized in space group I422
Components
  • Factor H-binding protein
  • JAR5 Heavy Chain
  • JAR5 Light Chain
KeywordsIMMUNE SYSTEM / Complex
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Factor H binding protein, C-terminal / : / : / Factor H binding protein, C-terminal / Factor H binding protein, N-terminal / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Factor H binding protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Neisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChesterman, C. / Malito, E. / Bottomley, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
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. / Mallet, C. / Bottomley, M.J. / van den Berg, R.A. / Faissol, D.
History
DepositionSep 26, 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JAR5 Heavy Chain
B: JAR5 Light Chain
H: JAR5 Heavy Chain
L: JAR5 Light Chain
C: Factor H-binding protein
D: Factor H-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,07331
Polymers158,2636
Non-polymers2,81025
Water00
1
A: JAR5 Heavy Chain
B: JAR5 Light Chain
D: Factor H-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,48115
Polymers79,1323
Non-polymers1,34912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-82 kcal/mol
Surface area30090 Å2
MethodPISA
2
H: JAR5 Heavy Chain
L: JAR5 Light Chain
C: Factor H-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,59316
Polymers79,1323
Non-polymers1,46113
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-95 kcal/mol
Surface area30480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.660, 167.660, 313.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Antibody JAR5 Heavy Chain


Mass: 27566.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody JAR5 Light Chain


Mass: 23865.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein Factor H-binding protein


Mass: 27699.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: E6MV22
#4: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Cd
Has ligand of interestN
Has protein modificationY

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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: 3.78 Å3/Da / Density % sol: 67.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Cadmium Chloride 0.1 M Sodium Acetate pH 4.6 30% PEG 300

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→49.27 Å / Num. obs: 49617 / % possible obs: 96.83 % / Redundancy: 13.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.5835 / Rrim(I) all: 0.6071 / Net I/σ(I): 9.48
Reflection shellResolution: 2.9→3.004 Å / Rmerge(I) obs: 4.16 / Num. unique obs: 4851 / CC1/2: 0.649 / Rrim(I) all: 4.318

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T5F

5t5f


Resolution: 2.9→49.27 Å / SU ML: 0.49 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 33.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2962 3818 7.69 %
Rwork0.2482 --
obs0.2518 49573 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10186 0 25 0 10211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310396
X-RAY DIFFRACTIONf_angle_d0.60914077
X-RAY DIFFRACTIONf_dihedral_angle_d23.3753765
X-RAY DIFFRACTIONf_chiral_restr0.0451569
X-RAY DIFFRACTIONf_plane_restr0.0061810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.930.3982480.3792929X-RAY DIFFRACTION100
2.93-2.970.40812360.37882819X-RAY DIFFRACTION100
2.97-30.40332430.36432881X-RAY DIFFRACTION100
3-3.040.38142440.34892908X-RAY DIFFRACTION100
3.04-3.080.38552440.32112921X-RAY DIFFRACTION100
3.08-3.120.38362400.32572896X-RAY DIFFRACTION100
3.12-3.170.37292450.3212919X-RAY DIFFRACTION100
3.17-3.220.38222440.33142880X-RAY DIFFRACTION100
3.22-3.270.44032390.33442885X-RAY DIFFRACTION100
3.27-3.320.34312480.31322934X-RAY DIFFRACTION100
3.32-3.380.35852420.3012917X-RAY DIFFRACTION100
3.38-3.440.29262410.26592884X-RAY DIFFRACTION100
3.44-3.50.32982410.24722921X-RAY DIFFRACTION100
3.5-3.580.33612400.24972886X-RAY DIFFRACTION100
3.58-3.650.27182370.24772909X-RAY DIFFRACTION100
3.65-3.740.31232480.25612918X-RAY DIFFRACTION100
3.74-3.830.31262530.24752878X-RAY DIFFRACTION100
3.83-3.940.30912330.25932911X-RAY DIFFRACTION100
3.94-4.050.29472470.24982895X-RAY DIFFRACTION100
4.05-4.180.24922540.22082925X-RAY DIFFRACTION100
4.18-4.330.29232340.20732893X-RAY DIFFRACTION100
4.33-4.50.27172410.1892900X-RAY DIFFRACTION100
4.5-4.710.20092400.18642902X-RAY DIFFRACTION100
4.71-4.960.24282340.19412927X-RAY DIFFRACTION100
4.96-5.270.30652470.20652908X-RAY DIFFRACTION100
5.27-5.670.25332420.2292912X-RAY DIFFRACTION100
5.67-6.240.31492440.24122909X-RAY DIFFRACTION100
6.24-7.140.33732400.26642903X-RAY DIFFRACTION100
7.15-8.990.25132340.24672927X-RAY DIFFRACTION100
9-49.270.27052320.2582871X-RAY DIFFRACTION98

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