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- PDB-8g1c: Crystal structure of polyreactive 3B03 human Fab -

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Basic information

Entry
Database: PDB / ID: 8g1c
TitleCrystal structure of polyreactive 3B03 human Fab
Components
  • Heavy chain of monoreactive 3B03 human Fab fragment
  • Light chain of monoreactive 3B03 human Fab fragment
KeywordsIMMUNE SYSTEM / immunoglobulin G / anti-influenza / monoreactive
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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: Heavy chain of monoreactive 3B03 human Fab fragment
B: Light chain of monoreactive 3B03 human Fab fragment
C: Heavy chain of monoreactive 3B03 human Fab fragment
D: Light chain of monoreactive 3B03 human Fab fragment


Theoretical massNumber of molelcules
Total (without water)93,0134
Polymers93,0134
Non-polymers00
Water15,565864
1
A: Heavy chain of monoreactive 3B03 human Fab fragment
B: Light chain of monoreactive 3B03 human Fab fragment


Theoretical massNumber of molelcules
Total (without water)46,5072
Polymers46,5072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-28 kcal/mol
Surface area18690 Å2
MethodPISA
2
C: Heavy chain of monoreactive 3B03 human Fab fragment
D: Light chain of monoreactive 3B03 human Fab fragment


Theoretical massNumber of molelcules
Total (without water)46,5072
Polymers46,5072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-26 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.420, 66.170, 90.238
Angle α, β, γ (deg.)104.090, 93.310, 91.600
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Antibody Heavy chain of monoreactive 3B03 human Fab fragment


Mass: 23529.236 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 Light chain of monoreactive 3B03 human Fab fragment


Mass: 22977.502 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.: 864 / 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: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 25% PEG4000, 0.2M Ammonium sulfate, 0.1M Sodium acetate pH 4.6

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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: 1.63→64.12 Å / Num. obs: 132793 / % possible obs: 88.47 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.81 Å2 / CC1/2: 0.643 / Net I/σ(I): 27.55
Reflection shellResolution: 1.632→1.69 Å / Num. unique obs: 13000 / CC1/2: 0.314

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→64.12 Å / SU ML: 0.1995 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.8376
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2358 2000 1.55 %
Rwork0.202 127063 -
obs0.2025 129063 88.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.1 Å2
Refinement stepCycle: LAST / Resolution: 1.63→64.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6435 0 0 864 7299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00636589
X-RAY DIFFRACTIONf_angle_d0.86258972
X-RAY DIFFRACTIONf_chiral_restr0.05831007
X-RAY DIFFRACTIONf_plane_restr0.00641154
X-RAY DIFFRACTIONf_dihedral_angle_d13.95792334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.670.35341440.33999077X-RAY DIFFRACTION88.46
1.67-1.720.28161320.29929090X-RAY DIFFRACTION88.86
1.72-1.770.29721450.27239097X-RAY DIFFRACTION88.65
1.77-1.830.27331540.2558955X-RAY DIFFRACTION87.18
1.83-1.890.29181270.24118763X-RAY DIFFRACTION85.27
1.89-1.970.23431300.22337994X-RAY DIFFRACTION78.24
1.97-2.060.2691360.21519074X-RAY DIFFRACTION88.39
2.06-2.160.26161460.21499422X-RAY DIFFRACTION91.6
2.16-2.30.26171570.21419357X-RAY DIFFRACTION91.33
2.3-2.480.25951490.21739259X-RAY DIFFRACTION90.13
2.48-2.730.23981300.21868812X-RAY DIFFRACTION85.95
2.73-3.120.24231540.20929036X-RAY DIFFRACTION88.2
3.12-3.930.24011540.17819738X-RAY DIFFRACTION94.82
3.93-64.120.16871420.15829389X-RAY DIFFRACTION91.49

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