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- PDB-8utk: IL-23R minibinder - 23R-B04dslf02IB -

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Basic information

Entry
Database: PDB / ID: 8utk
TitleIL-23R minibinder - 23R-B04dslf02IB
Components23R-B04dslf02IB
KeywordsDE NOVO PROTEIN / Computational design / selective inhibitors / IL-2 IL-17 cytokines DE NOVO PROTEIN
Function / homology1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Chem-PG6
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsBera, A.K. / Berger, S.A. / Kang, A. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2024
Title: Preclinical proof of principle for orally delivered Th17 antagonist miniproteins.
Authors: Berger, S. / Seeger, F. / Yu, T.Y. / Aydin, M. / Yang, H. / Rosenblum, D. / Guenin-Mace, L. / Glassman, C. / Arguinchona, L. / Sniezek, C. / Blackstone, A. / Carter, L. / Ravichandran, R. / ...Authors: Berger, S. / Seeger, F. / Yu, T.Y. / Aydin, M. / Yang, H. / Rosenblum, D. / Guenin-Mace, L. / Glassman, C. / Arguinchona, L. / Sniezek, C. / Blackstone, A. / Carter, L. / Ravichandran, R. / Ahlrichs, M. / Murphy, M. / Pultz, I.S. / Kang, A. / Bera, A.K. / Stewart, L. / Garcia, K.C. / Naik, S. / Spangler, J.B. / Beigel, F. / Siebeck, M. / Gropp, R. / Baker, D.
History
DepositionOct 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Aug 28, 2024Group: Database references / Category: citation / Item: _citation.page_last
Revision 1.3Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: 23R-B04dslf02IB
B: 23R-B04dslf02IB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3385
Polymers12,7972
Non-polymers5413
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-20 kcal/mol
Surface area7360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.414, 55.414, 85.834
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: Protein 23R-B04dslf02IB


Mass: 6398.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M Lithium sulfate 0.1 M Sodium acetate pH 4.5 and 50% (v/v) PEG 400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.94→47.99 Å / Num. obs: 11624 / % possible obs: 98.79 % / Redundancy: 20 % / Biso Wilson estimate: 38.93 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.511 / Rpim(I) all: 0.1164 / Net I/σ(I): 3.62
Reflection shellResolution: 1.94→2.009 Å / Redundancy: 20.4 % / Rmerge(I) obs: 2.587 / Mean I/σ(I) obs: 0.77 / Num. unique obs: 1121 / CC1/2: 0.372 / Rpim(I) all: 0.5828 / % possible all: 98.16

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→47.99 Å / SU ML: 0.254 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.6012
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2673 601 5.17 %
Rwork0.218 11020 -
obs0.2205 11621 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.43 Å2
Refinement stepCycle: LAST / Resolution: 1.94→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms872 0 31 25 928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064916
X-RAY DIFFRACTIONf_angle_d0.77181219
X-RAY DIFFRACTIONf_chiral_restr0.0386139
X-RAY DIFFRACTIONf_plane_restr0.0046143
X-RAY DIFFRACTIONf_dihedral_angle_d13.7059361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.140.32761520.32592672X-RAY DIFFRACTION98.09
2.14-2.440.28771430.20992701X-RAY DIFFRACTION98.51
2.44-3.080.2941570.24292751X-RAY DIFFRACTION99.05
3.08-47.990.24191490.19612896X-RAY DIFFRACTION99.54

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