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- PDB-8pjx: Crystal structure of the computationally designed SAKe6FR protein -

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Basic information

Entry
Database: PDB / ID: 8pjx
TitleCrystal structure of the computationally designed SAKe6FR protein
ComponentsSAKe6FR
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

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Assembly

Deposited unit
A: SAKe6FR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6574
Polymers31,5371
Non-polymers1203
Water3,747208
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)68.032, 68.032, 117.857
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw

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Components

#1: Protein SAKe6FR


Mass: 31536.516 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 43.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.19 M Calcium chloride, 0.095 M HEPES sodium salt pH 7.5, 26.6% (v/v) PEG 400, 5% (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: 1.7→48.11 Å / Num. obs: 31265 / % possible obs: 100 % / Redundancy: 17.8 % / Biso Wilson estimate: 28.74 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.011 / Rrim(I) all: 0.048 / Χ2: 1.01 / Net I/σ(I): 30.9 / Num. measured all: 557244
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 99.8 % / Redundancy: 17.9 % / Rmerge(I) obs: 1.018 / Num. measured all: 29177 / Num. unique obs: 1627 / CC1/2: 0.974 / Rpim(I) all: 0.246 / Rrim(I) all: 1.048 / Χ2: 0.97 / Net I/σ(I) obs: 3.2

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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→48.11 Å / SU ML: 0.1745 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.834
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1854 1555 5 %
Rwork0.182 29541 -
obs0.1821 31096 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.23 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2169 0 3 208 2380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00952293
X-RAY DIFFRACTIONf_angle_d1.16123151
X-RAY DIFFRACTIONf_chiral_restr0.081340
X-RAY DIFFRACTIONf_plane_restr0.0084416
X-RAY DIFFRACTIONf_dihedral_angle_d16.4039782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.31721490.23582590X-RAY DIFFRACTION99.02
1.76-1.820.30091240.23962647X-RAY DIFFRACTION99.11
1.82-1.890.24531480.22722626X-RAY DIFFRACTION99.36
1.89-1.980.19241400.18882635X-RAY DIFFRACTION99.5
1.98-2.080.17941270.17592647X-RAY DIFFRACTION99.64
2.08-2.210.17971440.19342659X-RAY DIFFRACTION99.75
2.21-2.380.18691280.19372692X-RAY DIFFRACTION99.93
2.38-2.620.20591400.19012697X-RAY DIFFRACTION99.93
2.62-30.20611460.18622702X-RAY DIFFRACTION100
3-3.780.17571480.1712754X-RAY DIFFRACTION99.97
3.78-48.110.16251610.1712892X-RAY DIFFRACTION99.87

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