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- PDB-8pjv: Crystal structure of the computationally designed SAKe6DR protein -

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Basic information

Entry
Database: PDB / ID: 8pjv
TitleCrystal structure of the computationally designed SAKe6DR protein
ComponentsSAKe6DR
KeywordsUNKNOWN FUNCTION / computational / design / scaffold / propeller / Kelch
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 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: SAKe6DR


Theoretical massNumber of molelcules
Total (without water)33,5631
Polymers33,5631
Non-polymers00
Water5,675315
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)76.932, 87.949, 78.373
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Components on special symmetry positions
IDModelComponents
11A-637-

HOH

21A-656-

HOH

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Components

#1: Protein SAKe6DR


Mass: 33563.473 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.: 315 / 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: 1.97 Å3/Da / Density % sol: 37.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.18 M Magnesium chloride, 0.09 M HEPES sodium salt pH 7.5, 27% (v/v) PEG 400, 10% (v/v) Glycerol

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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 EIGER2 XE 16M / Detector: PIXEL / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.14→46.57 Å / Num. obs: 96205 / % possible obs: 99.5 % / Redundancy: 8.8 % / Biso Wilson estimate: 13.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.016 / Rrim(I) all: 0.049 / Net I/σ(I): 19.6 / Num. measured all: 847426
Reflection shellResolution: 1.14→1.16 Å / % possible obs: 94.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.521 / Num. measured all: 27777 / Num. unique obs: 4463 / CC1/2: 0.913 / Rpim(I) all: 0.223 / Rrim(I) all: 0.569 / Net I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→46.57 Å / SU ML: 0.0995 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.5424
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.174 4745 4.94 %
Rwork0.1577 91384 -
obs0.1585 96129 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.14 Å2
Refinement stepCycle: LAST / Resolution: 1.14→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 0 315 2463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01142239
X-RAY DIFFRACTIONf_angle_d1.28823070
X-RAY DIFFRACTIONf_chiral_restr0.1011331
X-RAY DIFFRACTIONf_plane_restr0.0247412
X-RAY DIFFRACTIONf_dihedral_angle_d10.4889771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.26641370.22742846X-RAY DIFFRACTION92.35
1.15-1.170.24751530.21422984X-RAY DIFFRACTION97.7
1.17-1.180.22921590.2022961X-RAY DIFFRACTION98.92
1.18-1.20.18551620.19253000X-RAY DIFFRACTION98.94
1.2-1.210.19631480.16163000X-RAY DIFFRACTION99.12
1.21-1.230.18231520.15753013X-RAY DIFFRACTION99.06
1.23-1.250.20991640.15663044X-RAY DIFFRACTION99.5
1.25-1.260.18661530.15133014X-RAY DIFFRACTION99.25
1.26-1.280.17351500.14733022X-RAY DIFFRACTION99.65
1.28-1.30.1591520.14483052X-RAY DIFFRACTION99.56
1.3-1.330.16451530.14863041X-RAY DIFFRACTION99.53
1.33-1.350.17231510.15033039X-RAY DIFFRACTION99.75
1.35-1.380.17661310.15443052X-RAY DIFFRACTION99.81
1.38-1.410.18711520.15213028X-RAY DIFFRACTION99.87
1.41-1.440.18681490.15073068X-RAY DIFFRACTION99.84
1.44-1.470.16371550.14283039X-RAY DIFFRACTION100
1.47-1.510.16961600.14483081X-RAY DIFFRACTION100
1.51-1.550.1791650.13363031X-RAY DIFFRACTION99.97
1.55-1.590.14591630.13093027X-RAY DIFFRACTION99.97
1.59-1.640.18251730.14213053X-RAY DIFFRACTION100
1.64-1.70.17091690.14443057X-RAY DIFFRACTION100
1.7-1.770.15771880.14733042X-RAY DIFFRACTION99.97
1.77-1.850.17761700.14963049X-RAY DIFFRACTION100
1.85-1.950.15591650.14593085X-RAY DIFFRACTION100
1.95-2.070.16981570.13933070X-RAY DIFFRACTION100
2.07-2.230.15711680.14463086X-RAY DIFFRACTION99.97
2.23-2.460.17371640.15423089X-RAY DIFFRACTION100
2.46-2.810.16411450.1643143X-RAY DIFFRACTION99.97
2.81-3.540.1921590.16023124X-RAY DIFFRACTION99.82
3.54-46.570.17071780.17873244X-RAY DIFFRACTION99.62

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