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- PDB-8pjz: Crystal structure of the computationally designed SAKe6EEtal protein -

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Basic information

Entry
Database: PDB / ID: 8pjz
TitleCrystal structure of the computationally designed SAKe6EEtal protein
ComponentsSAKe6EEtal
KeywordsUNKNOWN FUNCTION / computational / design / scaffold / propeller / Kelch
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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

Downloads & links

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Assembly

Deposited unit
A: SAKe6EEtal
B: SAKe6EEtal


Theoretical massNumber of molelcules
Total (without water)64,7972
Polymers64,7972
Non-polymers00
Water5,603311
1
A: SAKe6EEtal


Theoretical massNumber of molelcules
Total (without water)32,3981
Polymers32,3981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAKe6EEtal


Theoretical massNumber of molelcules
Total (without water)32,3981
Polymers32,3981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.583, 50.047, 70.787
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Protein SAKe6EEtal


Mass: 32398.268 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.: 311 / 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: 1.89 Å3/Da / Density % sol: 34.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.2 M Ammonium acetate, 0.1 M Bis-Tris pH 5.5, 45% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 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: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→40.87 Å / Num. obs: 71635 / % possible obs: 94.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 16.46 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.033 / Rrim(I) all: 0.059 / Net I/σ(I): 11.1 / Num. measured all: 205437
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 94.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.43 / Num. measured all: 10201 / Num. unique obs: 3476 / CC1/2: 0.756 / Rpim(I) all: 0.3 / Rrim(I) all: 0.527 / Net I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→31.07 Å / SU ML: 0.1566 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.3799
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1902 3629 5.07 %
Rwork0.1703 67972 -
obs0.1713 71601 94.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.59 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 0 0 311 4643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01454447
X-RAY DIFFRACTIONf_angle_d1.47696074
X-RAY DIFFRACTIONf_chiral_restr0.103643
X-RAY DIFFRACTIONf_plane_restr0.0175809
X-RAY DIFFRACTIONf_dihedral_angle_d22.49111522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.29621130.24332632X-RAY DIFFRACTION94.49
1.52-1.540.24121320.20422547X-RAY DIFFRACTION94.5
1.54-1.560.21421350.20112668X-RAY DIFFRACTION94.82
1.56-1.590.21411680.1952593X-RAY DIFFRACTION94.52
1.59-1.610.20871660.19432679X-RAY DIFFRACTION94.99
1.61-1.640.23631740.1742617X-RAY DIFFRACTION95.22
1.64-1.670.23361560.1862545X-RAY DIFFRACTION95.04
1.67-1.70.24441450.18012670X-RAY DIFFRACTION95.49
1.7-1.730.29321020.18292746X-RAY DIFFRACTION95.44
1.73-1.760.22481740.17882560X-RAY DIFFRACTION95.76
1.76-1.80.22191580.15812650X-RAY DIFFRACTION95.58
1.8-1.840.21381310.18722715X-RAY DIFFRACTION96.15
1.84-1.890.20551180.1782601X-RAY DIFFRACTION95.07
1.89-1.940.22271870.15472605X-RAY DIFFRACTION94.61
1.94-20.20271340.14952582X-RAY DIFFRACTION94.27
2-2.060.17391380.16582646X-RAY DIFFRACTION94.53
2.06-2.140.16671220.17442629X-RAY DIFFRACTION94.47
2.14-2.220.2041700.16112588X-RAY DIFFRACTION94
2.22-2.320.16861340.17342626X-RAY DIFFRACTION93.27
2.32-2.450.15991240.18642615X-RAY DIFFRACTION93.45
2.45-2.60.21051450.19672555X-RAY DIFFRACTION93.33
2.6-2.80.19231240.1872546X-RAY DIFFRACTION91.72
2.8-3.080.18431580.16772528X-RAY DIFFRACTION91.14
3.08-3.520.19541090.16592550X-RAY DIFFRACTION90.94
3.53-4.440.15431130.14292607X-RAY DIFFRACTION93.34
4.44-31.070.155990.16532672X-RAY DIFFRACTION94.54

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