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- PDB-8bl3: De novo single-chain immunoglobulin dimer scIg12 -

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Basic information

Entry
Database: PDB / ID: 8bl3
TitleDe novo single-chain immunoglobulin dimer scIg12
ComponentsscIg12
KeywordsDE NOVO PROTEIN / de novo / immunoglobulin / single-chain dimer / sandwich / beta
Biological speciesEscherichia coli (E. coli)
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

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Assembly

Deposited unit
A: scIg12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2512
Polymers16,1591
Non-polymers921
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-0 kcal/mol
Surface area6850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.013, 72.013, 97.067
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein scIg12


Mass: 16159.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.89 Å3/Da / Density % sol: 68.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 45% v/v 2-methyl-2,4-pentanediol (MPD), 0.2 M calcium chloride, 0.1 M Bis-Tris at pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→48.53 Å / Num. obs: 6749 / % possible obs: 99.9 % / Redundancy: 11.4 % / CC1/2: 1 / Net I/σ(I): 16.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 12.1 % / Num. unique obs: 954 / CC1/2: 0.585

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: prediction

Resolution: 2.8→45.09 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.47 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.512 / SU Rfree Blow DPI: 0.334 / SU Rfree Cruickshank DPI: 0.331
RfactorNum. reflection% reflectionSelection details
Rfree0.2845 678 -RANDOM
Rwork0.2245 ---
obs0.2302 6712 100 %-
Displacement parametersBiso mean: 104.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.6793 Å20 Å20 Å2
2---0.6793 Å20 Å2
3---1.3585 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.8→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 0 6 17 1160
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0131165HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.251572HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d552SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes205HARMONIC5
X-RAY DIFFRACTIONt_it1165HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion143SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact822SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.75
X-RAY DIFFRACTIONt_other_torsion3.61
LS refinement shellResolution: 2.8→2.83 Å
RfactorNum. reflection% reflection
Rfree0.5924 20 -
Rwork0.4343 --
obs0.4494 204 99.51 %

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