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- PDB-9dd5: Crystal Structure of designed conformational switch effector pept... -

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Basic information

Entry
Database: PDB / ID: 9dd5
TitleCrystal Structure of designed conformational switch effector peptide CS221B
ComponentsDesigned conformational switch effector peptide CS221B
KeywordsDE NOVO PROTEIN / design model / Effector / kinetics and dynamics / Protein-protein interactions
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
B: Designed conformational switch effector peptide CS221B
A: Designed conformational switch effector peptide CS221B


Theoretical massNumber of molelcules
Total (without water)6,1832
Polymers6,1832
Non-polymers00
Water81145
1
B: Designed conformational switch effector peptide CS221B


Theoretical massNumber of molelcules
Total (without water)3,0921
Polymers3,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Designed conformational switch effector peptide CS221B


Theoretical massNumber of molelcules
Total (without water)3,0921
Polymers3,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.670, 25.091, 34.671
Angle α, β, γ (deg.)90.000, 102.771, 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/peptide Designed conformational switch effector peptide CS221B


Mass: 3091.635 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.88 Å3/Da / Density % sol: 34.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2 M Sodium chloride, 0.1M Na/K phosphate pH 6.2 and 50% (v/v) PEG 200

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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: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.5→33.81 Å / Num. obs: 7489 / % possible obs: 99.71 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.025 / Net I/σ(I): 12.57
Reflection shellResolution: 1.5→1.62 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 1.71 / Num. unique obs: 1451 / CC1/2: 0.992 / Rpim(I) all: 0.384 / % possible all: 99.38

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Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→33.81 Å / SU ML: 0.2021 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.3151
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2494 749 10 %
Rwork0.209 6739 -
obs0.2132 7488 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.43 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms430 0 0 45 475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044428
X-RAY DIFFRACTIONf_angle_d0.5997560
X-RAY DIFFRACTIONf_chiral_restr0.033966
X-RAY DIFFRACTIONf_plane_restr0.008668
X-RAY DIFFRACTIONf_dihedral_angle_d4.582252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.620.31151450.25051306X-RAY DIFFRACTION99.38
1.62-1.780.28161500.23281355X-RAY DIFFRACTION99.87
1.78-2.040.29811490.20661342X-RAY DIFFRACTION99.93
2.04-2.560.24981500.21011349X-RAY DIFFRACTION99.93
2.57-33.810.23191550.20271387X-RAY DIFFRACTION99.42
Refinement TLS params.Method: refined / Origin x: 1.03087929555 Å / Origin y: -6.21670397206 Å / Origin z: 14.7146747077 Å
111213212223313233
T0.156847672123 Å2-0.0228076570356 Å20.00201608403062 Å2-0.176044272909 Å2-0.0112651352007 Å2--0.173989557598 Å2
L2.95555434024 °2-0.404321834235 °21.06408840999 °2-2.27209475224 °2-0.17614484178 °2--4.9331826726 °2
S-0.0281019173832 Å °0.0627443800471 Å °0.0799699755872 Å °0.0350933440767 Å °0.0575363314243 Å °-0.139000491086 Å °-0.138622097942 Å °0.3685117939 Å °-0.0115625939156 Å °
Refinement TLS groupSelection details: all

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