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- PDB-9f8y: Crystal structure of a designed three-motif Respiratory Syncytial... -

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Basic information

Entry
Database: PDB / ID: 9f8y
TitleCrystal structure of a designed three-motif Respiratory Syncytial Virus immunogen
ComponentsRSVF-multi-3.5 designed scaffold
KeywordsDE NOVO PROTEIN / Designed immunogen / Specific Binding / RSV F protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCastro, K.M. / Correia, B.E.
Funding support Switzerland, European Union, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: Accurate single domain scaffolding of three non-overlapping protein epitopes using deep learning
Authors: Castro, K.M. / Watson, J.L. / Wang, J. / Southern, J. / Ayardulabi, R. / Georgeon, S. / Rosset, S. / Baker, D. / Correia, B.E.
History
DepositionMay 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: RSVF-multi-3.5 designed scaffold
A: RSVF-multi-3.5 designed scaffold
B: RSVF-multi-3.5 designed scaffold
C: RSVF-multi-3.5 designed scaffold


Theoretical massNumber of molelcules
Total (without water)67,3894
Polymers67,3894
Non-polymers00
Water1,11762
1
D: RSVF-multi-3.5 designed scaffold


Theoretical massNumber of molelcules
Total (without water)16,8471
Polymers16,8471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RSVF-multi-3.5 designed scaffold


Theoretical massNumber of molelcules
Total (without water)16,8471
Polymers16,8471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: RSVF-multi-3.5 designed scaffold


Theoretical massNumber of molelcules
Total (without water)16,8471
Polymers16,8471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: RSVF-multi-3.5 designed scaffold


Theoretical massNumber of molelcules
Total (without water)16,8471
Polymers16,8471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.843, 106.432, 113.589
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
RSVF-multi-3.5 designed scaffold


Mass: 16847.234 Da / Num. of mol.: 4
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.: 62 / 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: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium acetate, Tris pH 7.5, and 25 % (v/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.3→77.67 Å / Num. obs: 135054 / % possible obs: 99.26 % / Redundancy: 5.2 % / Biso Wilson estimate: 54.11 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.17
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 0.77 / Num. unique obs: 2558 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→77.67 Å / SU ML: 0.3831 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.2443
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2834 1364 5.27 %
Rwork0.2603 24516 -
obs0.2615 25880 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.97 Å2
Refinement stepCycle: LAST / Resolution: 2.3→77.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3685 0 0 62 3747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00863724
X-RAY DIFFRACTIONf_angle_d1.20245033
X-RAY DIFFRACTIONf_chiral_restr0.0804622
X-RAY DIFFRACTIONf_plane_restr0.0126640
X-RAY DIFFRACTIONf_dihedral_angle_d11.07481373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.39251350.34442416X-RAY DIFFRACTION99.96
2.38-2.480.37981310.33812448X-RAY DIFFRACTION100
2.48-2.590.38811350.34192427X-RAY DIFFRACTION99.96
2.59-2.720.32411430.29932414X-RAY DIFFRACTION99.65
2.72-2.90.32971440.29662429X-RAY DIFFRACTION99.88
2.9-3.120.2941210.30642466X-RAY DIFFRACTION99.92
3.12-3.430.31991430.28012372X-RAY DIFFRACTION98.24
3.44-3.930.30271420.252406X-RAY DIFFRACTION98.26
3.93-4.950.22941190.21212505X-RAY DIFFRACTION99.73
4.95-77.670.24431510.24392633X-RAY DIFFRACTION99.5

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