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- PDB-8pjt: Crystal structure of the computationally designed SAKe6DEref protein -

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Basic information

Entry
Database: PDB / ID: 8pjt
TitleCrystal structure of the computationally designed SAKe6DEref protein
ComponentsSAKe6DEref
KeywordsUNKNOWN FUNCTION / computational / design / scaffold / propeller / Kelch
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: SAKe6DEref
B: SAKe6DEref
C: SAKe6DEref
D: SAKe6DEref


Theoretical massNumber of molelcules
Total (without water)134,6874
Polymers134,6874
Non-polymers00
Water12,899716
1
A: SAKe6DEref


Theoretical massNumber of molelcules
Total (without water)33,6721
Polymers33,6721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAKe6DEref


Theoretical massNumber of molelcules
Total (without water)33,6721
Polymers33,6721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SAKe6DEref


Theoretical massNumber of molelcules
Total (without water)33,6721
Polymers33,6721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SAKe6DEref


Theoretical massNumber of molelcules
Total (without water)33,6721
Polymers33,6721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.531, 58.531, 78.706
Angle α, β, γ (deg.)90.000, 90.000, 82.150
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Protein
SAKe6DEref


Mass: 33671.637 Da / Num. of mol.: 4
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.: 716 / 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: 1.98 Å3/Da / Density % sol: 37.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.2 M Magnesium chloride, 0.1 M Tris pH 7, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.867023 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.867023 Å / Relative weight: 1
ReflectionResolution: 1.7→46.68 Å / Num. obs: 110541 / % possible obs: 97.1 % / Redundancy: 2.5 % / Biso Wilson estimate: 21.84 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.056 / Rrim(I) all: 0.091 / Χ2: 0.93 / Net I/σ(I): 7.5 / Num. measured all: 273253
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 95.4 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.391 / Num. measured all: 12941 / Num. unique obs: 5406 / CC1/2: 0.909 / Rpim(I) all: 0.305 / Rrim(I) all: 0.499 / Χ2: 0.93 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→39.35 Å / SU ML: 0.1871 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.5334
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2228 5238 4.74 %
Rwork0.1801 105240 -
obs0.1821 110478 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.67 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9082 0 0 716 9798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01189369
X-RAY DIFFRACTIONf_angle_d1.270712775
X-RAY DIFFRACTIONf_chiral_restr0.09061318
X-RAY DIFFRACTIONf_plane_restr0.01941739
X-RAY DIFFRACTIONf_dihedral_angle_d20.00773297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.2821900.24323549X-RAY DIFFRACTION95.41
1.72-1.740.2921540.24533372X-RAY DIFFRACTION95.5
1.74-1.760.30531820.21733430X-RAY DIFFRACTION95.71
1.76-1.780.23931490.23443550X-RAY DIFFRACTION95.8
1.78-1.810.32611890.25553380X-RAY DIFFRACTION95.5
1.81-1.830.28732040.2373519X-RAY DIFFRACTION96.23
1.83-1.860.26591720.22333393X-RAY DIFFRACTION95.99
1.86-1.890.24771720.2123561X-RAY DIFFRACTION96.29
1.89-1.910.25981500.19763416X-RAY DIFFRACTION96.12
1.91-1.950.23891240.18523541X-RAY DIFFRACTION96.63
1.95-1.980.22511580.17373494X-RAY DIFFRACTION96.54
1.98-2.020.20791790.17013521X-RAY DIFFRACTION96.28
2.02-2.050.20221790.18713442X-RAY DIFFRACTION96.71
2.05-2.10.26211580.19313535X-RAY DIFFRACTION96.83
2.1-2.140.24681670.18693496X-RAY DIFFRACTION97.08
2.14-2.190.27551380.19533569X-RAY DIFFRACTION96.71
2.19-2.250.20251700.1783540X-RAY DIFFRACTION97.04
2.25-2.310.27371690.17643473X-RAY DIFFRACTION97.17
2.31-2.370.28441780.1893526X-RAY DIFFRACTION97.63
2.38-2.450.27292010.19223517X-RAY DIFFRACTION97.46
2.45-2.540.20441630.19253554X-RAY DIFFRACTION97.76
2.54-2.640.24521900.18543499X-RAY DIFFRACTION97.77
2.64-2.760.21522100.1893535X-RAY DIFFRACTION97.81
2.76-2.910.22672280.16363461X-RAY DIFFRACTION97.98
2.91-3.090.20671880.18923543X-RAY DIFFRACTION98.34
3.09-3.330.20451800.17863539X-RAY DIFFRACTION98.33
3.33-3.660.20072180.17033582X-RAY DIFFRACTION98.55
3.66-4.190.18381690.14833549X-RAY DIFFRACTION98.57
4.19-5.280.1871330.14363615X-RAY DIFFRACTION98.79
5.28-39.350.21431760.19793539X-RAY DIFFRACTION98.05

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