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- PDB-7awy: Crystal structure of the computationally designed Scone-R protein -

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Basic information

Entry
Database: PDB / ID: 7awy
TitleCrystal structure of the computationally designed Scone-R protein
ComponentsScone-R
KeywordsDE NOVO PROTEIN / Beta-propeller / Computational design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMylemans, B. / Voet, A.R.D.
Funding support Belgium, 4items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)GBM-D3229-ASP/17 Belgium
Research Foundation - Flanders (FWO)G0E4717N Belgium
Research Foundation - Flanders (FWO)G051917N Belgium
Research Foundation - Flanders (FWO)G0F9316N Belgium
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Crystal structures of Scone: pseudosymmetric folding of a symmetric designer protein.
Authors: Mylemans, B. / Killian, T. / Vandebroek, L. / Van Meervelt, L. / Tame, J.R.H. / Parac-Vogt, T.N. / Voet, A.R.D.
History
DepositionNov 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.title / _citation.year
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Scone-R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5284
Polymers40,2521
Non-polymers2763
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-2 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.077, 79.834, 47.426
Angle α, β, γ (deg.)90.000, 100.984, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Scone-R


Mass: 40252.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M magnesium acetate 0.1 M sodium acetate 4% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.5→46.56 Å / Num. obs: 46828 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 20.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.019 / Rrim(I) all: 0.042 / Χ2: 0.9 / Net I/σ(I): 16.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2343 / CC1/2: 0.864 / Rpim(I) all: 0.278 / Rrim(I) all: 0.606 / Χ2: 0.78 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TJG

6tjg


Resolution: 1.5→46.56 Å / SU ML: 0.1513 / Cross valid method: FREE R-VALUE / σ(F): 0.61 / Phase error: 23.1709
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1908 2322 4.96 %
Rwork0.1625 44470 -
obs0.164 46792 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.22 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 18 343 2831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01452575
X-RAY DIFFRACTIONf_angle_d1.24483518
X-RAY DIFFRACTIONf_chiral_restr0.0821365
X-RAY DIFFRACTIONf_plane_restr0.0096449
X-RAY DIFFRACTIONf_dihedral_angle_d18.9138884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.28021320.26172596X-RAY DIFFRACTION99.24
1.53-1.560.28521340.24862598X-RAY DIFFRACTION99.27
1.56-1.60.2521240.23242633X-RAY DIFFRACTION99.39
1.6-1.640.26431200.21212596X-RAY DIFFRACTION99.74
1.64-1.680.26511280.20122634X-RAY DIFFRACTION99.78
1.68-1.730.22821230.19262595X-RAY DIFFRACTION99.82
1.73-1.790.231510.18982582X-RAY DIFFRACTION99.85
1.79-1.850.25091430.18252626X-RAY DIFFRACTION99.96
1.85-1.930.21021270.1722617X-RAY DIFFRACTION99.93
1.93-2.020.20671330.16172616X-RAY DIFFRACTION99.67
2.02-2.120.20071500.16342613X-RAY DIFFRACTION99.96
2.12-2.260.20961420.16312611X-RAY DIFFRACTION99.96
2.26-2.430.18781470.16332598X-RAY DIFFRACTION100
2.43-2.670.19791480.16692633X-RAY DIFFRACTION100
2.67-3.060.18651390.16482616X-RAY DIFFRACTION100
3.06-3.860.15351310.14262633X-RAY DIFFRACTION100
3.86-46.560.16131500.14062673X-RAY DIFFRACTION99.79

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