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- PDB-8pjq: Crystal structure of the SAKe2BE protein -

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Basic information

Entry
Database: PDB / ID: 8pjq
TitleCrystal structure of the SAKe2BE protein
ComponentsSAKe2BE
KeywordsUNKNOWN FUNCTION / computational / design / scaffold / propeller / Kelch
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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: SAKe2BE


Theoretical massNumber of molelcules
Total (without water)10,4401
Polymers10,4401
Non-polymers00
Water1,27971
1
A: SAKe2BE

A: SAKe2BE

A: SAKe2BE


Theoretical massNumber of molelcules
Total (without water)31,3213
Polymers31,3213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6010 Å2
ΔGint-26 kcal/mol
Surface area10480 Å2
Unit cell
Length a, b, c (Å)44.226, 44.226, 70.274
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-260-

HOH

21A-263-

HOH

31A-271-

HOH

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Components

#1: Protein SAKe2BE


Mass: 10440.465 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.: 71 / 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: 1.9 Å3/Da / Density % sol: 35.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.018 M Calcium chloride, 0.09 M Sodium acetate pH 4.6, 27% (v/v) MPD, 10% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.867023 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.867023 Å / Relative weight: 1
ReflectionResolution: 1.15→38.3 Å / Num. obs: 28974 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 11.88 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.013 / Rrim(I) all: 0.059 / Χ2: 0.97 / Net I/σ(I): 24.1 / Num. measured all: 568939
Reflection shellResolution: 1.15→1.17 Å / % possible obs: 100 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.757 / Num. measured all: 28623 / Num. unique obs: 1444 / CC1/2: 0.949 / Rpim(I) all: 0.174 / Rrim(I) all: 0.777 / Χ2: 0.96 / Net I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→35.14 Å / SU ML: 0.1254 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4434
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1845 1476 5.1 %
Rwork0.1791 27480 -
obs0.1793 28956 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.84 Å2
Refinement stepCycle: LAST / Resolution: 1.15→35.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms683 0 0 71 754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133777
X-RAY DIFFRACTIONf_angle_d1.83811069
X-RAY DIFFRACTIONf_chiral_restr0.1202119
X-RAY DIFFRACTIONf_plane_restr0.0097142
X-RAY DIFFRACTIONf_dihedral_angle_d12.8674262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.190.24371380.22512466X-RAY DIFFRACTION100
1.19-1.230.20491220.19332477X-RAY DIFFRACTION99.88
1.23-1.280.22981170.18042454X-RAY DIFFRACTION100
1.28-1.340.24531470.16782451X-RAY DIFFRACTION99.77
1.34-1.410.2261310.17622472X-RAY DIFFRACTION99.92
1.41-1.50.22751320.18142462X-RAY DIFFRACTION100
1.5-1.610.18141160.16352497X-RAY DIFFRACTION99.96
1.61-1.770.17631380.1752515X-RAY DIFFRACTION100
1.77-2.030.16631410.16752485X-RAY DIFFRACTION99.96
2.03-2.560.15781250.17272549X-RAY DIFFRACTION100
2.56-35.140.18081690.18652652X-RAY DIFFRACTION99.93

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