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- PDB-8pju: Crystal structure of the computationally designed SAKe6DEtal protein -

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Basic information

Entry
Database: PDB / ID: 8pju
TitleCrystal structure of the computationally designed SAKe6DEtal protein
ComponentsSAKe6DEtal
KeywordsUNKNOWN FUNCTION / computational / design / scaffold / propeller / Kelch
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsWouters, S.M.L.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1S89918N Belgium
Research Foundation - Flanders (FWO)G0F9316N Belgium
Research Foundation - Flanders (FWO)G051917N Belgium
CitationJournal: To Be Published
Title: Computational design of the SAKe scaffold proteins
Authors: Wouters, S.M.L. / Noguchi, H. / Voet, A.R.D.
History
DepositionJun 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAKe6DEtal


Theoretical massNumber of molelcules
Total (without water)33,2541
Polymers33,2541
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.435, 78.007, 85.884
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2

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Components

#1: Protein SAKe6DEtal


Mass: 33254.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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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: 1.92 Å3/Da / Density % sol: 36.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.2 M Lithium sulfate, 0.1 M bis-Tris pH 5.5, 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.72→46.07 Å / Num. obs: 27630 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 20.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.03 / Rrim(I) all: 0.099 / Net I/σ(I): 16 / Num. measured all: 295871
Reflection shellResolution: 1.72→1.75 Å / % possible obs: 99.8 % / Redundancy: 10.6 % / Rmerge(I) obs: 1.078 / Num. measured all: 15275 / Num. unique obs: 1436 / CC1/2: 0.878 / Rpim(I) all: 0.346 / Rrim(I) all: 1.135 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→35.51 Å / SU ML: 0.2084 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1529
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233 1419 5.15 %
Rwork0.1972 26159 -
obs0.199 27578 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.01 Å2
Refinement stepCycle: LAST / Resolution: 1.72→35.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 0 108 2094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01412031
X-RAY DIFFRACTIONf_angle_d1.39312771
X-RAY DIFFRACTIONf_chiral_restr0.2999304
X-RAY DIFFRACTIONf_plane_restr0.0149364
X-RAY DIFFRACTIONf_dihedral_angle_d21.6723712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.780.3711340.30142581X-RAY DIFFRACTION99.71
1.78-1.850.31011480.2382570X-RAY DIFFRACTION99.74
1.85-1.940.28381410.21282568X-RAY DIFFRACTION99.85
1.94-2.040.23481520.20472585X-RAY DIFFRACTION99.82
2.04-2.170.25671430.18322599X-RAY DIFFRACTION99.96
2.17-2.330.20971300.18632598X-RAY DIFFRACTION99.85
2.33-2.570.24831320.2052625X-RAY DIFFRACTION99.89
2.57-2.940.26691390.19612633X-RAY DIFFRACTION99.96
2.94-3.70.2081490.18642650X-RAY DIFFRACTION100
3.71-35.510.20021510.18892750X-RAY DIFFRACTION99.79

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