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- PDB-7r20: Anti-Arc nanobody E5 -

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Basic information

Entry
Database: PDB / ID: 7r20
TitleAnti-Arc nanobody E5
ComponentsAnti-Arc nanobody E5
KeywordsIMMUNE SYSTEM / Nanobody / VHH
Biological speciesVicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsMarkusson, S. / Kursula, P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway249951 Norway
CitationJournal: Plos One / Year: 2022
Title: High-affinity anti-Arc nanobodies provide tools for structural and functional studies.
Authors: Markusson, S. / Hallin, E.I. / Bustad, H.J. / Raasakka, A. / Xu, J. / Muruganandam, G. / Loris, R. / Martinez, A. / Bramham, C.R. / Kursula, P.
History
DepositionFeb 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Anti-Arc nanobody E5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,70411
Polymers12,7671
Non-polymers93710
Water84747
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-47 kcal/mol
Surface area6810 Å2
Unit cell
Length a, b, c (Å)45.900, 45.900, 103.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Antibody Anti-Arc nanobody E5


Mass: 12767.269 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.26 M (NH4)2SO4, 0.1 M LiSO4 and 0.1 M Tris-HCl pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.42→41.98 Å / Num. obs: 201623 / % possible obs: 99.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 24.51 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.108 / Net I/σ(I): 9.5
Reflection shellResolution: 1.42→1.46 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 0.3 / Num. unique obs: 21801 / CC1/2: 0.333 / Rrim(I) all: 5.687 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIXdev_3958refinement
XDSFeb 5, 2021data reduction
XSCALEFeb 5, 2021data scaling
PHASER2.8.3.phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HVG

5hvg


Resolution: 1.42→41.98 Å / SU ML: 0.2566 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.7126
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2367 1981 9.21 %
Rwork0.185 19531 -
obs0.1897 21512 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.08 Å2
Refinement stepCycle: LAST / Resolution: 1.42→41.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms885 0 56 47 988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121005
X-RAY DIFFRACTIONf_angle_d1.27351361
X-RAY DIFFRACTIONf_chiral_restr0.0955140
X-RAY DIFFRACTIONf_plane_restr0.0075175
X-RAY DIFFRACTIONf_dihedral_angle_d16.092364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.460.5421270.54691271X-RAY DIFFRACTION91.73
1.46-1.490.51931380.49291340X-RAY DIFFRACTION98.47
1.49-1.540.43451410.40411384X-RAY DIFFRACTION99.74
1.54-1.590.40191390.34581376X-RAY DIFFRACTION99.67
1.59-1.650.38881390.32631376X-RAY DIFFRACTION98.7
1.65-1.710.36551410.27611377X-RAY DIFFRACTION99.22
1.71-1.790.30111370.22821356X-RAY DIFFRACTION99.27
1.79-1.880.24441410.16991396X-RAY DIFFRACTION99.61
1.88-20.22481430.13781401X-RAY DIFFRACTION99.17
2-2.160.21851400.14131386X-RAY DIFFRACTION99.41
2.16-2.370.20321450.12881417X-RAY DIFFRACTION99.62
2.37-2.720.20461460.15121437X-RAY DIFFRACTION99.94
2.72-3.420.21081450.16931450X-RAY DIFFRACTION99.75
3.42-41.980.21561590.17831564X-RAY DIFFRACTION99.94

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