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- PDB-6u50: Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan ... -

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Basic information

Entry
Database: PDB / ID: 6u50
TitleAnti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB)
ComponentsAnti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB)
KeywordsIMMUNE SYSTEM / Antibody / nanobody / Ebola / filovirus
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1752
Polymers13,0561
Non-polymers1181
Water1,54986
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)47.839, 47.839, 85.378
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Antibody Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB)


Mass: 13056.438 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: pecan219 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 37.5% precipitant mix (2-methyl-2,4-pentanediol, polyethylene glycol [PEG] 1000, PEG 3350), 0.1 M amino acids mix (glutamate, alanine, glycine, lysine, serine), 0.1 M HEPES/MOPS pH 7.5 ...Details: 37.5% precipitant mix (2-methyl-2,4-pentanediol, polyethylene glycol [PEG] 1000, PEG 3350), 0.1 M amino acids mix (glutamate, alanine, glycine, lysine, serine), 0.1 M HEPES/MOPS pH 7.5 {Molecular Dimensions Morpheus HT-96 Condition H8}

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→42.69 Å / Num. obs: 15558 / % possible obs: 99.4 % / Redundancy: 9.7 % / Biso Wilson estimate: 17.62 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.045 / Rrim(I) all: 0.142 / Net I/σ(I): 12.1
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2140 / CC1/2: 0.367 / Rpim(I) all: 0.605 / Rrim(I) all: 1.82 / % possible all: 96.2

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Processing

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

6u51


Resolution: 1.6→37.27 Å / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.2285
RfactorNum. reflection% reflection
Rfree0.214 1567 10.1 %
Rwork0.1689 --
obs0.1736 15516 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.46 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms866 0 8 86 960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094893
X-RAY DIFFRACTIONf_angle_d0.96061210
X-RAY DIFFRACTIONf_chiral_restr0.0848130
X-RAY DIFFRACTIONf_plane_restr0.0052161
X-RAY DIFFRACTIONf_dihedral_angle_d13.6357334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.33131320.2631189X-RAY DIFFRACTION95.38
1.65-1.710.29981400.21221252X-RAY DIFFRACTION100
1.71-1.780.25721440.19471260X-RAY DIFFRACTION100
1.78-1.860.24441330.17521240X-RAY DIFFRACTION100
1.86-1.950.24151410.15681246X-RAY DIFFRACTION100
1.95-2.080.18921470.13911275X-RAY DIFFRACTION100
2.08-2.240.18921420.13781259X-RAY DIFFRACTION100
2.24-2.460.2471440.15821265X-RAY DIFFRACTION100
2.46-2.820.2071410.16971293X-RAY DIFFRACTION100
2.82-3.550.21591450.16551300X-RAY DIFFRACTION100
3.55-37.270.18311580.17471370X-RAY DIFFRACTION99.48

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