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- PDB-6u53: Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire ... -

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Basic information

Entry
Database: PDB / ID: 6u53
TitleAnti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire C (ZC)
ComponentsAnti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire C (ZC)
KeywordsIMMUNE SYSTEM / Antibody / nanobody / Ebola / filovirus
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsTaylor, A.B. / Sherwood, L.J. / Hart, P.J. / Hayhurst, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI112851 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI105568 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)C06 RR012087 United States
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Paratope Duality and Gullying are Among the Atypical Recognition Mechanisms Used by a Trio of Nanobodies to Differentiate Ebolavirus Nucleoproteins.
Authors: Sherwood, L.J. / Taylor, A.B. / Hart, P.J. / Hayhurst, A.
History
DepositionAug 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire C (ZC)


Theoretical massNumber of molelcules
Total (without water)13,3771
Polymers13,3771
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.414, 78.414, 37.811
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Antibody Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire C (ZC)


Mass: 13376.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Semi-synthetic single pot library Nomad 1 based upon Lama glama
Source: (gene. exp.) Lama glama (llama) / Plasmid: pecan73 / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1.0 M sodium/potassium tartrate, 0.2 M lithium sulfate, 0.1M Tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.49→31.24 Å / Num. obs: 13542 / % possible obs: 68.3 % / Redundancy: 12.3 % / Biso Wilson estimate: 29.18 Å2 / CC1/2: 1 / Rpim(I) all: 0.012 / Rrim(I) all: 0.043 / Net I/σ(I): 23.3
Reflection shellResolution: 1.49→1.58 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 678 / CC1/2: 0.557 / Rpim(I) all: 0.555 / Rrim(I) all: 1.97 / % possible all: 21.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U51

6u51


Resolution: 1.49→31.24 Å / SU ML: 0.2049 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 38.3306
RfactorNum. reflection% reflection
Rfree0.2491 1351 10.01 %
Rwork0.1877 --
obs0.1938 13503 68.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.87 Å2
Refinement stepCycle: LAST / Resolution: 1.49→31.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 0 0 66 1000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091048
X-RAY DIFFRACTIONf_angle_d1.12731429
X-RAY DIFFRACTIONf_chiral_restr0.0846146
X-RAY DIFFRACTIONf_plane_restr0.0067191
X-RAY DIFFRACTIONf_dihedral_angle_d15.564375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.540.4194340.323307X-RAY DIFFRACTION17.71
1.54-1.610.4427590.2765529X-RAY DIFFRACTION30.22
1.61-1.680.2858760.2726690X-RAY DIFFRACTION39.46
1.68-1.770.32361000.2887899X-RAY DIFFRACTION51.57
1.77-1.880.29791290.251164X-RAY DIFFRACTION65.97
1.88-2.020.26971530.20731375X-RAY DIFFRACTION78.28
2.02-2.230.26981870.20951675X-RAY DIFFRACTION93.95
2.23-2.550.3011980.20381782X-RAY DIFFRACTION99.95
2.55-3.210.27492010.20361816X-RAY DIFFRACTION100
3.21-31.240.21132140.161915X-RAY DIFFRACTION99.72

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