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- PDB-9dd2: Crystal Structure of Designed allosteric facilitated dissociation... -

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Basic information

Entry
Database: PDB / ID: 9dd2
TitleCrystal Structure of Designed allosteric facilitated dissociation switch AS5
ComponentsDesigned 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: 1.72 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


Theoretical massNumber of molelcules
Total (without water)30,3041
Polymers30,3041
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.379, 62.379, 78.501
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Designed allosteric facilitated dissociation switch AS5 H


Mass: 30303.742 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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 Matthews: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Sodium acetate pH 5.0, 20% (v/v) MPD

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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: 1.72→48.84 Å / Num. obs: 31981 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 32 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.017 / Net I/σ(I): 18.5
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1667 / CC1/2: 0.875 / Rpim(I) all: 0.263 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→48.84 Å / SU ML: 0.2175 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.99
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.243 1990 6.23 %
Rwork0.2034 29957 -
obs0.2058 31947 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.72 Å2
Refinement stepCycle: LAST / Resolution: 1.72→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 0 125 2104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562014
X-RAY DIFFRACTIONf_angle_d0.682712
X-RAY DIFFRACTIONf_chiral_restr0.0458328
X-RAY DIFFRACTIONf_plane_restr0.0067354
X-RAY DIFFRACTIONf_dihedral_angle_d14.2185787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.760.31931420.27542139X-RAY DIFFRACTION100
1.76-1.810.32321360.26982122X-RAY DIFFRACTION100
1.81-1.860.31121430.27472126X-RAY DIFFRACTION99.96
1.86-1.920.35691450.29562127X-RAY DIFFRACTION99.96
1.92-1.990.31661470.27662141X-RAY DIFFRACTION100
1.99-2.070.27791340.24252134X-RAY DIFFRACTION100
2.07-2.170.25061430.232134X-RAY DIFFRACTION100
2.17-2.280.26331440.23582142X-RAY DIFFRACTION100
2.28-2.420.26041430.21142111X-RAY DIFFRACTION100
2.42-2.610.26681390.22442158X-RAY DIFFRACTION100
2.61-2.870.25851410.22032144X-RAY DIFFRACTION100
2.88-3.290.22411470.20832137X-RAY DIFFRACTION100
3.29-4.140.20851420.18032161X-RAY DIFFRACTION99.96
4.15-48.840.22331440.16192181X-RAY DIFFRACTION99.96

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