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- PDB-9dd1: Designed allosteric facilitated dissociation switch AS1 in comple... -

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Basic information

Entry
Database: PDB / ID: 9dd1
TitleDesigned allosteric facilitated dissociation switch AS1 in complex state THE with methylated lysines
Components
  • Designed allosteric facilitated dissociation switch AS1 E
  • Designed allosteric facilitated dissociation switch AS1 H
  • Designed allosteric facilitated dissociation switch AS1 T
KeywordsDE NOVO PROTEIN / design model / Effector / kinetics and dynamics / Protein-protein interactions
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsBera, A.K. / Broerman, A. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Design of facilitated dissociation enables temporal control over cytokine signaling
Authors: Broerman, A. / Bera, A.K. / Baker, D.
History
DepositionAug 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Designed allosteric facilitated dissociation switch AS1 T
B: Designed allosteric facilitated dissociation switch AS1 E
C: Designed allosteric facilitated dissociation switch AS1 H


Theoretical massNumber of molelcules
Total (without water)45,8253
Polymers45,8253
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-30 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.859, 110.859, 65.532
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: Protein Designed allosteric facilitated dissociation switch AS1 T


Mass: 28796.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide Designed allosteric facilitated dissociation switch AS1 E


Mass: 3022.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Protein Designed allosteric facilitated dissociation switch AS1 H


Mass: 14006.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
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: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1 M Citric acid pH 3.5 and 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97936 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2024
Details: Horizontal pre-focus bimorph mirror & KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 3.7→28.21 Å / Num. obs: 10334 / % possible obs: 100 % / Redundancy: 11.8 % / Biso Wilson estimate: 102.53 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.057 / Net I/σ(I): 10.7
Reflection shellResolution: 3.7→3.93 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.951 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 1717 / CC1/2: 0.692 / Rpim(I) all: 0.28 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→28.21 Å / SU ML: 0.5483 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.4481
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2772 828 9.96 %
Rwork0.2472 7488 -
obs0.2503 8316 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.53 Å2
Refinement stepCycle: LAST / Resolution: 3.7→28.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3062 0 0 0 3062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00163077
X-RAY DIFFRACTIONf_angle_d0.38974144
X-RAY DIFFRACTIONf_chiral_restr0.0336502
X-RAY DIFFRACTIONf_plane_restr0.0028520
X-RAY DIFFRACTIONf_dihedral_angle_d15.60481169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.930.3011440.30151250X-RAY DIFFRACTION100
3.93-4.230.32571320.23881238X-RAY DIFFRACTION100
4.24-4.660.28891380.22931253X-RAY DIFFRACTION100
4.66-5.330.29151410.25431241X-RAY DIFFRACTION100
5.33-6.70.31141400.30421240X-RAY DIFFRACTION100
6.7-28.210.22131330.21431266X-RAY DIFFRACTION100

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