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- PDB-8fzo: Crystal structure of polyreactive 338E6 mouse Fab -

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Basic information

Entry
Database: PDB / ID: 8fzo
TitleCrystal structure of polyreactive 338E6 mouse Fab
Components
  • 338E6 Fab heavy chain
  • 338E6 Fab light chain
KeywordsIMMUNE SYSTEM / Polyreactivity / Polyspecificity / Fab / Immunoglobulin A
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsBorowska, M.T. / Adams, E.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI147954 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI115471 United States
CitationJournal: Cell Rep / Year: 2023
Title: Biochemical and biophysical characterization of natural polyreactivity in antibodies.
Authors: Borowska, M.T. / Boughter, C.T. / Bunker, J.J. / Guthmiller, J.J. / Wilson, P.C. / Roux, B. / Bendelac, A. / Adams, E.J.
History
DepositionJan 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 338E6 Fab heavy chain
B: 338E6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,5362
Polymers47,5362
Non-polymers00
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-26 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.920, 59.650, 82.250
Angle α, β, γ (deg.)90.000, 99.100, 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: Antibody 338E6 Fab heavy chain


Mass: 24062.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)
#2: Antibody 338E6 Fab light chain


Mass: 23472.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O
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: 2.09 Å3/Da / Density % sol: 41.01 % / Description: rod
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 29% PEG 3000, 0.1M Sodium Sulfate, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.83→81.21 Å / Num. obs: 33933 / % possible obs: 97.38 % / Redundancy: 32.1 % / Biso Wilson estimate: 14.93 Å2 / CC1/2: 0.903 / CC star: 0.974 / Net I/σ(I): 21.6
Reflection shellResolution: 1.83→1.895 Å / Num. unique obs: 3289 / CC1/2: 0.731

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→81.21 Å / SU ML: 0.1953 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7832
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2197 1622 4.79 %
Rwork0.1725 32261 -
obs0.1748 33883 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.29 Å2
Refinement stepCycle: LAST / Resolution: 1.83→81.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 0 0 462 3705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00623317
X-RAY DIFFRACTIONf_angle_d0.8854505
X-RAY DIFFRACTIONf_chiral_restr0.061504
X-RAY DIFFRACTIONf_plane_restr0.0067575
X-RAY DIFFRACTIONf_dihedral_angle_d6.0869457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.880.26691420.20192617X-RAY DIFFRACTION95.17
1.88-1.940.2611410.17442653X-RAY DIFFRACTION96.34
1.94-2.010.211270.15692640X-RAY DIFFRACTION96.44
2.01-2.090.20241320.16112625X-RAY DIFFRACTION96.8
2.09-2.190.21061260.16722703X-RAY DIFFRACTION97.28
2.19-2.30.25431240.17692690X-RAY DIFFRACTION97.1
2.3-2.450.25031380.1792669X-RAY DIFFRACTION97.53
2.45-2.640.24981430.18472678X-RAY DIFFRACTION98.16
2.64-2.90.21521350.18532739X-RAY DIFFRACTION98.22
2.9-3.320.23611430.17952682X-RAY DIFFRACTION98.09
3.32-4.180.17471270.15882769X-RAY DIFFRACTION98.74
4.19-81.210.2011440.16742796X-RAY DIFFRACTION98.56

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