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- PDB-9dd3: Crystal Structure of Designed allosteric facilitated dissociation... -

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Basic information

Entry
Database: PDB / ID: 9dd3
TitleCrystal Structure of Designed allosteric facilitated dissociation switch AS5 in complex state HE
Components
  • Designed allosteric facilitated dissociation switch AS5 E
  • Designed allosteric facilitated dissociation switch AS5 H
KeywordsDE NOVO PROTEIN / design model / Effector / kinetics and dynamics / Protein-protein interactions
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 AS5 H
B: Designed allosteric facilitated dissociation switch AS5 E


Theoretical massNumber of molelcules
Total (without water)31,5712
Polymers31,5712
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-21 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.171, 35.663, 75.522
Angle α, β, γ (deg.)90.000, 116.200, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Designed allosteric facilitated dissociation switch AS5 H


Mass: 28478.879 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 AS5 E


Mass: 3091.635 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
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 % sol: 28.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5 and 25% w/v Polyethylene glycol 3,350

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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: 0.92009 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2023
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: 0.92009 Å / Relative weight: 1
ReflectionResolution: 1.64→31.69 Å / Num. obs: 24348 / % possible obs: 91.01 % / Redundancy: 1.9 % / Biso Wilson estimate: 28.07 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.054 / Net I/σ(I): 6.62
Reflection shellResolution: 1.64→1.68 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.062 / Num. unique obs: 1919 / CC1/2: 0.717 / Rpim(I) all: 0.054 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→31.69 Å / SU ML: 0.2351 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.6189
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2514 1855 7.62 %
Rwork0.202 22493 -
obs0.2059 24348 91.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.23 Å2
Refinement stepCycle: LAST / Resolution: 1.64→31.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 0 70 2202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032161
X-RAY DIFFRACTIONf_angle_d0.52472905
X-RAY DIFFRACTIONf_chiral_restr0.0368355
X-RAY DIFFRACTIONf_plane_restr0.0045374
X-RAY DIFFRACTIONf_dihedral_angle_d3.8101302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.34561460.32381773X-RAY DIFFRACTION95
1.68-1.730.33931480.30271793X-RAY DIFFRACTION94.45
1.73-1.790.29381470.27311780X-RAY DIFFRACTION94.6
1.79-1.850.34051470.25481779X-RAY DIFFRACTION94.13
1.85-1.930.30581440.24731749X-RAY DIFFRACTION93.71
1.93-2.020.29561450.23841759X-RAY DIFFRACTION93.15
2.02-2.120.29031440.20591749X-RAY DIFFRACTION91.49
2.12-2.250.27231390.19191695X-RAY DIFFRACTION89.86
2.26-2.430.23251400.19511692X-RAY DIFFRACTION89.06
2.43-2.670.2881420.19921720X-RAY DIFFRACTION90.39
2.67-3.060.25451400.20011696X-RAY DIFFRACTION88.91
3.06-3.850.21091370.19081663X-RAY DIFFRACTION86.33
3.85-31.690.22741360.18011645X-RAY DIFFRACTION82.72

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