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- PDB-9dcx: Crystal Structure of designed allosteric facilitated dissociation... -

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Basic information

Entry
Database: PDB / ID: 9dcx
TitleCrystal Structure of designed allosteric facilitated dissociation switch AS1
ComponentsDesigned allosteric facilitated dissociation switch AS1 H
KeywordsDE NOVO PROTEIN / design model / Effector / kinetics and dynamics / Protein-protein interactions
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7572
Polymers28,7221
Non-polymers351
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.546, 61.546, 236.103
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Designed allosteric facilitated dissociation switch AS1 H


Mass: 28721.518 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium cacodylate pH 6.5 and 50 % v/v PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.8→48.58 Å / Num. obs: 25501 / % possible obs: 99.31 % / Redundancy: 12.7 % / Biso Wilson estimate: 32.5 Å2 / CC1/2: 0.955 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.018 / Net I/σ(I): 22.53
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.945 / Mean I/σ(I) obs: 8.59 / Num. unique obs: 1764 / CC1/2: 0.673 / Rpim(I) all: 0.246 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.58 Å / SU ML: 0.2186 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.8516
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2565 2000 7.84 %
Rwork0.2134 23501 -
obs0.2168 25501 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.69 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1965 0 2 92 2059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751973
X-RAY DIFFRACTIONf_angle_d0.80362648
X-RAY DIFFRACTIONf_chiral_restr0.0484329
X-RAY DIFFRACTIONf_plane_restr0.0068337
X-RAY DIFFRACTIONf_dihedral_angle_d13.5523778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.33161380.28861626X-RAY DIFFRACTION100
1.85-1.890.31481400.28741645X-RAY DIFFRACTION100
1.89-1.950.53671300.41091528X-RAY DIFFRACTION92.83
1.95-2.010.28121410.25581653X-RAY DIFFRACTION100
2.01-2.090.38361390.28021642X-RAY DIFFRACTION99.83
2.09-2.170.26691410.22381651X-RAY DIFFRACTION99.83
2.17-2.270.29791410.23581656X-RAY DIFFRACTION98.74
2.27-2.390.24171410.19391650X-RAY DIFFRACTION99.33
2.39-2.540.25081430.19431684X-RAY DIFFRACTION99.95
2.54-2.730.24121420.21411674X-RAY DIFFRACTION100
2.73-3.010.28051450.22971698X-RAY DIFFRACTION99.95
3.01-3.440.26311470.19931729X-RAY DIFFRACTION99.89
3.44-4.340.20731490.18591754X-RAY DIFFRACTION100
4.34-48.580.23631630.20161911X-RAY DIFFRACTION99.95

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