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- PDB-8f8v: Crystal structure of Nb.X0 -

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Basic information

Entry
Database: PDB / ID: 8f8v
TitleCrystal structure of Nb.X0
ComponentsNb.X0
KeywordsIMMUNE SYSTEM / nanobody / glycobiology / immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesCamelidae mixed library (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsGoldgur, Y. / Ravetch, J. / Gupta, A. / Kao, K. / Andi, B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007739 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI111825 United States
Bill & Melinda Gates FoundationINV-034057 United States
CitationJournal: Nat Commun / Year: 2023
Title: Mechanism of glycoform specificity and in vivo protection by an anti-afucosylated IgG nanobody.
Authors: Gupta, A. / Kao, K.S. / Yamin, R. / Oren, D.A. / Goldgur, Y. / Du, J. / Lollar, P. / Sundberg, E.J. / Ravetch, J.V.
History
DepositionNov 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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: Nb.X0
B: Nb.X0


Theoretical massNumber of molelcules
Total (without water)26,2112
Polymers26,2112
Non-polymers00
Water3,153175
1
A: Nb.X0


Theoretical massNumber of molelcules
Total (without water)13,1061
Polymers13,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nb.X0


Theoretical massNumber of molelcules
Total (without water)13,1061
Polymers13,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.310, 95.081, 110.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-240-

HOH

21B-223-

HOH

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Components

#1: Antibody Nb.X0


Mass: 13105.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae mixed library (mammal)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 % v/v PPGBA 400 + 15 % v/v 1-Propanol. Cryopreserved with 40% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.8→50.32 Å / Num. obs: 27855 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 24.95 Å2 / CC1/2: 0.991 / Rpim(I) all: 0.045 / Net I/σ(I): 27.7
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 1313 / CC1/2: 0.708 / Rpim(I) all: 0.339

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→50.32 Å / SU ML: 0.1849 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7857
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2216 2000 7.18 %
Rwork0.1918 25838 -
obs0.1939 27838 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.99 Å2
Refinement stepCycle: LAST / Resolution: 1.81→50.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 0 175 2021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711890
X-RAY DIFFRACTIONf_angle_d0.9532564
X-RAY DIFFRACTIONf_chiral_restr0.0581266
X-RAY DIFFRACTIONf_plane_restr0.0076332
X-RAY DIFFRACTIONf_dihedral_angle_d6.1438274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.860.2829990.28931276X-RAY DIFFRACTION67.93
1.86-1.910.27181400.2471819X-RAY DIFFRACTION97.41
1.91-1.970.28711460.22711873X-RAY DIFFRACTION98.92
1.97-2.030.24321420.21491844X-RAY DIFFRACTION99.4
2.03-2.10.24741440.20281852X-RAY DIFFRACTION99.8
2.1-2.190.25641470.19321897X-RAY DIFFRACTION99.95
2.19-2.290.22281450.19291880X-RAY DIFFRACTION99.85
2.29-2.410.23321450.20171875X-RAY DIFFRACTION99.95
2.41-2.560.23161470.20861900X-RAY DIFFRACTION99.95
2.56-2.760.21921460.20861882X-RAY DIFFRACTION99.95
2.76-3.030.22721480.1951916X-RAY DIFFRACTION100
3.03-3.470.18281470.1921898X-RAY DIFFRACTION99.46
3.47-4.370.21031480.17041905X-RAY DIFFRACTION98.42
4.37-50.320.21261560.172021X-RAY DIFFRACTION99.63

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