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- PDB-8pjy: Crystal structure of the computationally designed SAKe6EEref protein -

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Basic information

Entry
Database: PDB / ID: 8pjy
TitleCrystal structure of the computationally designed SAKe6EEref protein
ComponentsSAKe6EEref
KeywordsUNKNOWN FUNCTION / computational / design / scaffold / propeller / Kelch
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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: SAKe6EEref


Theoretical massNumber of molelcules
Total (without water)31,0051
Polymers31,0051
Non-polymers00
Water5,891327
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)47.048, 66.661, 48.243
Angle α, β, γ (deg.)90.000, 117.590, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein SAKe6EEref


Mass: 31005.018 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.: 327 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.2 M Ammonium acetate, 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: Diamond / Beamline: I04 / Wavelength: 0.97857 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: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.3→42.76 Å / Num. obs: 64797 / % possible obs: 99.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 13.52 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.02 / Rrim(I) all: 0.044 / Net I/σ(I): 18.4 / Num. measured all: 300926
Reflection shellResolution: 1.3→1.32 Å / % possible obs: 99.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.645 / Num. measured all: 15047 / Num. unique obs: 3261 / CC1/2: 0.835 / Rpim(I) all: 0.332 / Rrim(I) all: 0.728 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→42.76 Å / SU ML: 0.1019 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.4071
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1549 3265 5.04 %
Rwork0.1361 61498 -
obs0.1371 64763 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.62 Å2
Refinement stepCycle: LAST / Resolution: 1.3→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 0 0 327 2481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832223
X-RAY DIFFRACTIONf_angle_d1.12743063
X-RAY DIFFRACTIONf_chiral_restr0.0952343
X-RAY DIFFRACTIONf_plane_restr0.0094404
X-RAY DIFFRACTIONf_dihedral_angle_d11.4921755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.22541240.20282662X-RAY DIFFRACTION99.89
1.32-1.340.18451280.18092697X-RAY DIFFRACTION99.86
1.34-1.360.21981580.17722612X-RAY DIFFRACTION99.96
1.36-1.390.21331260.17252716X-RAY DIFFRACTION99.86
1.39-1.410.18571210.16232652X-RAY DIFFRACTION99.96
1.41-1.440.19821570.16032636X-RAY DIFFRACTION99.93
1.44-1.470.20521530.15772672X-RAY DIFFRACTION99.86
1.47-1.50.15851100.14072686X-RAY DIFFRACTION99.96
1.5-1.530.16851390.12842671X-RAY DIFFRACTION99.89
1.53-1.570.13951450.11992680X-RAY DIFFRACTION99.93
1.57-1.610.15331190.12212693X-RAY DIFFRACTION100
1.61-1.660.15351420.12162663X-RAY DIFFRACTION99.89
1.66-1.720.1471690.12442643X-RAY DIFFRACTION99.93
1.72-1.780.15411510.12632676X-RAY DIFFRACTION99.89
1.78-1.850.13851420.1272648X-RAY DIFFRACTION99.96
1.85-1.930.14211600.1222663X-RAY DIFFRACTION99.96
1.93-2.030.13311290.11552696X-RAY DIFFRACTION99.93
2.03-2.160.15361410.12312679X-RAY DIFFRACTION100
2.16-2.330.14971510.12192673X-RAY DIFFRACTION99.96
2.33-2.560.15341460.1382683X-RAY DIFFRACTION100
2.56-2.930.14111630.1322674X-RAY DIFFRACTION99.75
2.93-3.70.15371270.13942705X-RAY DIFFRACTION99.72
3.7-42.760.15721640.1482718X-RAY DIFFRACTION99.52

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