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- PDB-8bl6: De novo single-chain immunoglobulin dimer scIg12+EF3a -

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Basic information

Entry
Database: PDB / ID: 8bl6
TitleDe novo single-chain immunoglobulin dimer scIg12+EF3a
ComponentsdIG14-scdim-EF62
KeywordsDE NOVO PROTEIN / de novo / immunoglobulin / single-chain dimer / sandwich / beta / EF-hand
Function / homologyTERBIUM(III) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNadal, M. / Roel-Touris, J. / Marcos, E.
Funding supportEuropean Union, Spain, 2items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 145-2021European Union
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Nat Commun / Year: 2023
Title: Single-chain dimers from de novo immunoglobulins as robust scaffolds for multiple binding loops.
Authors: Roel-Touris, J. / Nadal, M. / Marcos, E.
History
DepositionNov 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dIG14-scdim-EF62
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7105
Polymers20,1411
Non-polymers5694
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-23 kcal/mol
Surface area7370 Å2
Unit cell
Length a, b, c (Å)73.841, 73.841, 96.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein dIG14-scdim-EF62


Mass: 20141.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Tb
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: 4.07 Å3/Da / Density % sol: 69.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG MME 2000 20.0%w/v, TRIS 0.1M pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.50102 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2022
RadiationMonochromator: 1.50102 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.50102 Å / Relative weight: 1
ReflectionResolution: 2.8→58.59 Å / Num. obs: 7030 / % possible obs: 100 % / Redundancy: 16.2 % / CC1/2: 0.944 / Rmerge(I) obs: 0.016 / Net I/σ(I): 15.4
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 1001 / CC1/2: 0.876

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model prediction

Resolution: 2.8→58.59 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.006 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.483 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25711 724 10.4 %RANDOM
Rwork0.20182 ---
obs0.20744 6261 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.072 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0 Å20 Å2
2--0.6 Å20 Å2
3----1.19 Å2
Refinement stepCycle: 1 / Resolution: 2.8→58.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1135 0 9 0 1144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131162
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171081
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.6671566
X-RAY DIFFRACTIONr_angle_other_deg1.1221.592505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8365137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56321.02678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.36615208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1511514
X-RAY DIFFRACTIONr_chiral_restr0.0630.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021303
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02259
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.389.239554
X-RAY DIFFRACTIONr_mcbond_other8.279.22552
X-RAY DIFFRACTIONr_mcangle_it12.05513.853689
X-RAY DIFFRACTIONr_mcangle_other11.96913.858689
X-RAY DIFFRACTIONr_scbond_it10.71910.713605
X-RAY DIFFRACTIONr_scbond_other10.71510.718606
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.81415.537875
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 55 -
Rwork0.381 441 -
obs--99.6 %

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