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- PDB-8g1b: Crystal structure of polyreactive 2G02 human Fab -

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Basic information

Entry
Database: PDB / ID: 8g1b
TitleCrystal structure of polyreactive 2G02 human Fab
Components
  • The heavy chain of human 2G02 Fab fragment
  • The light chain of human 2G02 Fab fragment
KeywordsIMMUNE SYSTEM / immunoglobulin G / anti-influenza / polyreactivity / polyspecificity
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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
Revision 1.1Oct 23, 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: The heavy chain of human 2G02 Fab fragment
B: The light chain of human 2G02 Fab fragment
C: The heavy chain of human 2G02 Fab fragment
D: The light chain of human 2G02 Fab fragment


Theoretical massNumber of molelcules
Total (without water)95,4264
Polymers95,4264
Non-polymers00
Water11,566642
1
A: The heavy chain of human 2G02 Fab fragment
B: The light chain of human 2G02 Fab fragment


Theoretical massNumber of molelcules
Total (without water)47,7132
Polymers47,7132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-21 kcal/mol
Surface area19170 Å2
MethodPISA
2
C: The heavy chain of human 2G02 Fab fragment
D: The light chain of human 2G02 Fab fragment


Theoretical massNumber of molelcules
Total (without water)47,7132
Polymers47,7132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-23 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.160, 59.440, 99.280
Angle α, β, γ (deg.)90.000, 98.830, 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 The heavy chain of human 2G02 Fab fragment


Mass: 23692.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody The light chain of human 2G02 Fab fragment


Mass: 24020.811 Da / Num. of mol.: 2
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.: 642 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M Magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.67→69.33 Å / Num. obs: 92961 / % possible obs: 96.38 % / Redundancy: 1.9 % / Biso Wilson estimate: 16.28 Å2 / CC1/2: 0.943 / Net I/σ(I): 7.22
Reflection shellResolution: 1.67→1.73 Å / Num. unique obs: 9082 / CC1/2: 0.171

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→69.33 Å / SU ML: 0.2032 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.6047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.222 1936 2.14 %
Rwork0.1942 88590 -
obs0.1948 90526 96.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.01 Å2
Refinement stepCycle: LAST / Resolution: 1.67→69.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6654 0 0 642 7296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00576807
X-RAY DIFFRACTIONf_angle_d0.84239263
X-RAY DIFFRACTIONf_chiral_restr0.05421041
X-RAY DIFFRACTIONf_plane_restr0.00751192
X-RAY DIFFRACTIONf_dihedral_angle_d14.15582451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.710.31911210.28015690X-RAY DIFFRACTION86.93
1.71-1.760.28521280.25275899X-RAY DIFFRACTION90.56
1.76-1.810.29171300.23576018X-RAY DIFFRACTION92.2
1.81-1.870.28061320.22576071X-RAY DIFFRACTION93.11
1.87-1.930.29481340.22086222X-RAY DIFFRACTION95.19
1.93-2.010.25961380.21296277X-RAY DIFFRACTION96.45
2.01-2.10.25881420.20296460X-RAY DIFFRACTION98.6
2.1-2.210.22961430.19216467X-RAY DIFFRACTION98.92
2.22-2.350.21321440.19866552X-RAY DIFFRACTION99.41
2.35-2.540.24611420.20156470X-RAY DIFFRACTION99.15
2.54-2.790.21221430.2026518X-RAY DIFFRACTION99.08
2.79-3.190.23451450.19576596X-RAY DIFFRACTION99.87
3.19-4.020.18381450.16926599X-RAY DIFFRACTION99.88
4.03-69.330.17461490.16526751X-RAY DIFFRACTION99.8

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