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- PDB-8g19: Crystal structure of monoreactive 4C05 human Fab -

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Basic information

Entry
Database: PDB / ID: 8g19
TitleCrystal structure of monoreactive 4C05 human Fab
Components
  • Heavy chain of anti-influenza human 4C05 Fab fragment
  • Light chain of anti-influenza human 4C05 Fab fragment
KeywordsIMMUNE SYSTEM / immunoglobulin G / anti-influenza / monoreactive
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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
DepositionFeb 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Light chain of anti-influenza human 4C05 Fab fragment
H: Heavy chain of anti-influenza human 4C05 Fab fragment


Theoretical massNumber of molelcules
Total (without water)46,6962
Polymers46,6962
Non-polymers00
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-27 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.839, 70.609, 87.680
Angle α, β, γ (deg.)90.000, 108.950, 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
Components on special symmetry positions
IDModelComponents
11H-362-

HOH

21H-527-

HOH

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Components

#1: Antibody Light chain of anti-influenza human 4C05 Fab fragment


Mass: 22573.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Heavy chain of anti-influenza human 4C05 Fab fragment


Mass: 24122.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 5000 MME, 0.2M Ammonium sulfate, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.77→39.54 Å / Num. obs: 44160 / % possible obs: 98.04 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.35 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.61
Reflection shellResolution: 1.77→1.833 Å / Num. unique obs: 4398 / CC1/2: 0.924

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→39.54 Å / SU ML: 0.1932 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3259
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2194 2104 4.76 %
Rwork0.187 42056 -
obs0.1886 44160 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.35 Å2
Refinement stepCycle: LAST / Resolution: 1.77→39.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 0 351 3632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073365
X-RAY DIFFRACTIONf_angle_d1.01684600
X-RAY DIFFRACTIONf_chiral_restr0.063522
X-RAY DIFFRACTIONf_plane_restr0.0075585
X-RAY DIFFRACTIONf_dihedral_angle_d6.53470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.26271320.21592805X-RAY DIFFRACTION98.52
1.81-1.860.24171400.20772823X-RAY DIFFRACTION98.8
1.86-1.910.25271450.21132810X-RAY DIFFRACTION98.76
1.91-1.960.22331590.19642754X-RAY DIFFRACTION98.35
1.96-2.020.26791220.19832797X-RAY DIFFRACTION98.12
2.03-2.10.22561180.19752794X-RAY DIFFRACTION97.49
2.1-2.180.24051010.19492686X-RAY DIFFRACTION93.43
2.18-2.280.23331530.19912840X-RAY DIFFRACTION99.24
2.28-2.40.23271320.20492839X-RAY DIFFRACTION99.03
2.4-2.550.25891580.20982814X-RAY DIFFRACTION99
2.55-2.750.23261480.21062820X-RAY DIFFRACTION98.97
2.75-3.020.24181440.20222769X-RAY DIFFRACTION97.2
3.02-3.460.21071440.18282762X-RAY DIFFRACTION96.54
3.46-4.360.19811320.15692905X-RAY DIFFRACTION99.87
4.36-39.540.17711760.16212838X-RAY DIFFRACTION97.6

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