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- PDB-9dd0: Designed allosteric facilitated dissociation switch AS1 in comple... -

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Basic information

Entry
Database: PDB / ID: 9dd0
TitleDesigned allosteric facilitated dissociation switch AS1 in complex state TH with methylated lysines, crystal #2
Components
  • 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: 3.88 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 H
C: Designed allosteric facilitated dissociation switch AS1 H
B: Designed allosteric facilitated dissociation switch AS1 T
D: Designed allosteric facilitated dissociation switch AS1 T


Theoretical massNumber of molelcules
Total (without water)88,1054
Polymers88,1054
Non-polymers00
Water00
1
A: Designed allosteric facilitated dissociation switch AS1 H
B: Designed allosteric facilitated dissociation switch AS1 T


Theoretical massNumber of molelcules
Total (without water)44,0522
Polymers44,0522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-2 kcal/mol
Surface area17980 Å2
MethodPISA
2
C: Designed allosteric facilitated dissociation switch AS1 H
D: Designed allosteric facilitated dissociation switch AS1 T


Theoretical massNumber of molelcules
Total (without water)44,0522
Polymers44,0522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-2 kcal/mol
Surface area17500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.977, 74.068, 211.773
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Designed allosteric facilitated dissociation switch AS1 H


Mass: 29283.525 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: Protein Designed allosteric facilitated dissociation switch AS1 T


Mass: 14768.834 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)
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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8 M Ammonium citrate tribasic pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 13, 2024 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 3.88→30.24 Å / Num. obs: 9716 / % possible obs: 99.8 % / Redundancy: 9.6 % / Biso Wilson estimate: 122 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.27 / Rpim(I) all: 0.091 / Net I/σ(I): 5.8
Reflection shellResolution: 3.88→4.08 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2448 / CC1/2: 0.892 / Rpim(I) all: 0.246 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_5246refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.88→29.09 Å / SU ML: 0.5023 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 29.4208
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2789 966 9.99 %
Rwork0.2261 8702 -
obs0.2314 9668 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 114.68 Å2
Refinement stepCycle: LAST / Resolution: 3.88→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5891 0 0 0 5891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00325923
X-RAY DIFFRACTIONf_angle_d0.51497974
X-RAY DIFFRACTIONf_chiral_restr0.0365956
X-RAY DIFFRACTIONf_plane_restr0.00361013
X-RAY DIFFRACTIONf_dihedral_angle_d13.43992266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.88-4.080.32961340.27431210X-RAY DIFFRACTION100
4.08-4.340.30731350.25291216X-RAY DIFFRACTION100
4.34-4.670.29391360.23551224X-RAY DIFFRACTION99.85
4.67-5.140.29551360.2261227X-RAY DIFFRACTION99.93
5.14-5.880.33451370.26241232X-RAY DIFFRACTION100
5.88-7.390.3331410.26691265X-RAY DIFFRACTION99.86
7.39-29.090.20851470.17411328X-RAY DIFFRACTION99.8

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