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- PDB-8upb: De novo designed IL-6 mimetic -

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Basic information

Entry
Database: PDB / ID: 8upb
TitleDe novo designed IL-6 mimetic
ComponentsDe novo designed IL-6 mimetic
KeywordsCYTOKINE / de novo design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsBorowska, M.T. / Jude, K.M. / Garcia, K.C.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1-AI51321 United States
The Mark Foundation United States
CitationJournal: Nat Commun / Year: 2024
Title: De novo design of miniprotein antagonists of cytokine storm inducers.
Authors: Huang, B. / Coventry, B. / Borowska, M.T. / Arhontoulis, D.C. / Exposit, M. / Abedi, M. / Jude, K.M. / Halabiya, S.F. / Allen, A. / Cordray, C. / Goreshnik, I. / Ahlrichs, M. / Chan, S. / ...Authors: Huang, B. / Coventry, B. / Borowska, M.T. / Arhontoulis, D.C. / Exposit, M. / Abedi, M. / Jude, K.M. / Halabiya, S.F. / Allen, A. / Cordray, C. / Goreshnik, I. / Ahlrichs, M. / Chan, S. / Tunggal, H. / DeWitt, M. / Hyams, N. / Carter, L. / Stewart, L. / Fuller, D.H. / Mei, Y. / Garcia, K.C. / Baker, D.
History
DepositionOct 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo designed IL-6 mimetic


Theoretical massNumber of molelcules
Total (without water)7,8261
Polymers7,8261
Non-polymers00
Water1,20767
1
A: De novo designed IL-6 mimetic

A: De novo designed IL-6 mimetic


Theoretical massNumber of molelcules
Total (without water)15,6522
Polymers15,6522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2020 Å2
ΔGint-15 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.010, 47.010, 74.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-162-

HOH

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Components

#1: Protein De novo designed IL-6 mimetic


Mass: 7826.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1M Tri-sodium citrate, 0.1M Sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.48→39.71 Å / Num. obs: 14459 / % possible obs: 99.88 % / Redundancy: 2 % / Biso Wilson estimate: 24.15 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.35
Reflection shellResolution: 1.48→1.533 Å / Num. unique obs: 1385 / CC1/2: 0.539

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→39.71 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 1445 10 %
Rwork0.2039 --
obs0.2065 14455 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.48→39.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms552 0 0 67 619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007583
X-RAY DIFFRACTIONf_angle_d0.912784
X-RAY DIFFRACTIONf_dihedral_angle_d10.239236
X-RAY DIFFRACTIONf_chiral_restr0.05586
X-RAY DIFFRACTIONf_plane_restr0.008103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.530.35471390.34371245X-RAY DIFFRACTION100
1.53-1.590.32041420.29021275X-RAY DIFFRACTION100
1.59-1.670.2541410.23541279X-RAY DIFFRACTION100
1.67-1.750.26851410.24121271X-RAY DIFFRACTION100
1.75-1.860.29091440.23781289X-RAY DIFFRACTION100
1.86-2.010.23381430.20931285X-RAY DIFFRACTION100
2.01-2.210.21031440.19591296X-RAY DIFFRACTION100
2.21-2.530.22191450.17371311X-RAY DIFFRACTION100
2.53-3.190.23581490.21281338X-RAY DIFFRACTION100
3.19-39.710.20881570.19111421X-RAY DIFFRACTION100

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