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- PDB-7ax0: Crystal structure of the computationally designed Scone-E protein... -

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Basic information

Entry
Database: PDB / ID: 7ax0
TitleCrystal structure of the computationally designed Scone-E protein co-crystallized with STA form a
ComponentsSconeE
KeywordsDE NOVO PROTEIN / Beta-propeller / Computational design
Function / homologyPHOSPHATE ION / Keggin (STA)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMylemans, B. / Vandebroek, L. / Parac-Vogt, T.N. / 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 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Jan 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: SconeE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1814
Polymers40,1171
Non-polymers3,0643
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodGel filtration
2
A: SconeE
hetero molecules

A: SconeE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3628
Polymers80,2342
Non-polymers6,1286
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area2500 Å2
ΔGint-23 kcal/mol
Surface area23980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.270, 88.270, 194.987
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein SconeE


Mass: 40116.891 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-SIW / Keggin (STA)


Mass: 2874.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O40SiW12 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.8M Na/K phosphate 3.5 mM STA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→71.17 Å / Num. obs: 43141 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 42.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.039 / Rrim(I) all: 0.146 / Χ2: 0.97 / Net I/σ(I): 16.7
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 11.3 % / Rmerge(I) obs: 1.77 / Mean I/σ(I) obs: 3 / Num. unique obs: 4026 / CC1/2: 0.919 / Rpim(I) all: 0.53 / Χ2: 0.97 / % possible all: 100

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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: 2.2→71.17 Å / SU ML: 0.2776 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.906
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2398 2118 4.91 %
Rwork0.2076 41023 -
obs0.2092 43141 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.39 Å2
Refinement stepCycle: LAST / Resolution: 2.2→71.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 63 119 2631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01052602
X-RAY DIFFRACTIONf_angle_d1.29293661
X-RAY DIFFRACTIONf_chiral_restr0.0671372
X-RAY DIFFRACTIONf_plane_restr0.0069442
X-RAY DIFFRACTIONf_dihedral_angle_d19.639881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.31171630.27732718X-RAY DIFFRACTION99.97
2.25-2.310.3091300.25152741X-RAY DIFFRACTION99.97
2.31-2.370.38071380.25532729X-RAY DIFFRACTION100
2.37-2.440.27881330.24722742X-RAY DIFFRACTION100
2.44-2.520.29311360.24812772X-RAY DIFFRACTION100
2.52-2.610.29591350.24562729X-RAY DIFFRACTION99.97
2.61-2.710.30431420.25152725X-RAY DIFFRACTION100
2.71-2.840.32381270.2682748X-RAY DIFFRACTION99.97
2.84-2.990.28031560.24512715X-RAY DIFFRACTION99.97
2.99-3.170.27981330.22532745X-RAY DIFFRACTION100
3.17-3.420.24421640.20942718X-RAY DIFFRACTION100
3.42-3.760.24911290.19442730X-RAY DIFFRACTION100
3.76-4.310.22151420.1662736X-RAY DIFFRACTION100
4.31-5.420.13841390.14742746X-RAY DIFFRACTION100
5.43-71.170.22231510.21952729X-RAY DIFFRACTION99.69

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