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- PDB-8ulh: Fab of RSV neutralizing antibody 1G12 -

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Basic information

Entry
Database: PDB / ID: 8ulh
TitleFab of RSV neutralizing antibody 1G12
Components
  • 1G12 Fab heavy chain
  • 1G12 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / neutralizing / antibody / RSV / antiviral / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsHarshbarger, W.D. / Andreano, E. / Malito, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Structural and functional properties of monoclonal and vaccine-induced antibodies targeting epitopes of emerging RSV variants
Authors: Xian, Y. / Andreano, E. / Tian, S. / Phung, E. / Garbinski, L. / Biancucci, M. / Lofano, G. / Mallett, C.P. / Balsaraf, A. / Huang, Y. / Buricchi, F. / Finco, O. / Rappuoli, R. / Bottomley, ...Authors: Xian, Y. / Andreano, E. / Tian, S. / Phung, E. / Garbinski, L. / Biancucci, M. / Lofano, G. / Mallett, C.P. / Balsaraf, A. / Huang, Y. / Buricchi, F. / Finco, O. / Rappuoli, R. / Bottomley, M.J. / Chandramouli, S. / Warter, L. / Williams, J. / Malito, E. / Harshbarger, W.D.
History
DepositionOct 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 1G12 Fab heavy chain
L: 1G12 Fab light chain


Theoretical massNumber of molelcules
Total (without water)50,6592
Polymers50,6592
Non-polymers00
Water12,592699
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-25 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.456, 82.563, 112.234
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody 1G12 Fab heavy chain


Mass: 27343.318 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 1G12 Fab light chain


Mass: 23316.137 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.: 699 / 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: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 10 mM Hepes pH 7.5, 150 mM NaCl, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→34.08 Å / Num. obs: 66305 / % possible obs: 95.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 12.95 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.67
Reflection shellResolution: 1.692→1.753 Å / Num. unique obs: 4543 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
HKL-30001.20.1_4487data reduction
PHENIX1.20.1_4487refinement
HKL-3000data scaling
PHENIXphasing
PHENIX1.20.1-4487refinement
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→34.08 Å / SU ML: 0.1808 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3308
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2276 3138 3.18 %
Rwork0.194 95641 -
obs0.1951 63223 77.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.84 Å2
Refinement stepCycle: LAST / Resolution: 1.69→34.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3247 0 0 699 3946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01163330
X-RAY DIFFRACTIONf_angle_d1.2054539
X-RAY DIFFRACTIONf_chiral_restr0.0664511
X-RAY DIFFRACTIONf_plane_restr0.0093579
X-RAY DIFFRACTIONf_dihedral_angle_d28.3378459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.720.3033580.30711778X-RAY DIFFRACTION31.47
1.72-1.750.2757720.27222178X-RAY DIFFRACTION39.12
1.75-1.780.2968770.25362386X-RAY DIFFRACTION42.73
1.78-1.810.2842830.24242491X-RAY DIFFRACTION44.51
1.81-1.840.3103880.23192747X-RAY DIFFRACTION48.99
1.84-1.880.26521050.23223124X-RAY DIFFRACTION56.12
1.88-1.920.25551140.22163385X-RAY DIFFRACTION60.13
1.92-1.970.2431210.21553603X-RAY DIFFRACTION64.81
1.97-2.020.19191310.18224088X-RAY DIFFRACTION72.59
2.02-2.070.19941440.18374369X-RAY DIFFRACTION78.53
2.07-2.130.21891620.18154790X-RAY DIFFRACTION86.51
2.13-2.20.23491770.18695211X-RAY DIFFRACTION93.01
2.2-2.280.25641750.19095476X-RAY DIFFRACTION97.73
2.28-2.370.19741830.20185552X-RAY DIFFRACTION99.24
2.37-2.480.27131800.20235552X-RAY DIFFRACTION99.12
2.48-2.610.22631820.20425481X-RAY DIFFRACTION97.96
2.61-2.770.21251820.20895594X-RAY DIFFRACTION99.83
2.77-2.990.27721730.20195579X-RAY DIFFRACTION99.83
2.99-3.290.24231880.19245592X-RAY DIFFRACTION99.9
3.29-3.760.21361860.17565599X-RAY DIFFRACTION99.93
3.76-4.740.18961830.16235515X-RAY DIFFRACTION99.01
4.74-34.080.21021740.19695551X-RAY DIFFRACTION99.07

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