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- PDB-6tjg: Crystal structure of the computationally designed Cake8 protein -

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Basic information

Entry
Database: PDB / ID: 6tjg
TitleCrystal structure of the computationally designed Cake8 protein
ComponentsCake8
KeywordsDE NOVO PROTEIN / Beta-propeller / computationally designed / symmetrical / repeat protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLaier, I. / Mylemans, B. / Noguchi, H. / Voet, A.R.D.
Funding support Belgium, 4items
OrganizationGrant numberCountry
Research Foundation - FlandersGBM-D3229-ASP/17 Belgium
Research Foundation - FlandersG0E4717N Belgium
Research Foundation - FlandersG051917N Belgium
Research Foundation - FlandersG0F9316N Belgium
CitationJournal: Febs J. / Year: 2021
Title: Structural plasticity of a designer protein sheds light on beta-propeller protein evolution.
Authors: Mylemans, B. / Laier, I. / Kamata, K. / Akashi, S. / Noguchi, H. / Tame, J.R.H. / Voet, A.R.D.
History
DepositionNov 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cake8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1444
Polymers34,7891
Non-polymers3553
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-19 kcal/mol
Surface area12560 Å2
Unit cell
Length a, b, c (Å)34.368, 65.897, 71.027
Angle α, β, γ (deg.)90.000, 92.640, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Cake8


Mass: 34789.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.18M Magnesium acetate, 0.09M Sodium, Cacodylate pH 6.5, 27% MPD, 15% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→48.28 Å / Num. obs: 29356 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 24.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.034 / Rrim(I) all: 0.076 / Χ2: 0.83 / Net I/σ(I): 12.2
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1704 / CC1/2: 0.972 / Rpim(I) all: 0.18 / Rrim(I) all: 0.4 / Χ2: 0.53 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computationally designed model cake8

Resolution: 1.8→35.48 Å / SU ML: 0.1833 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1086
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2246 1627 5.56 %
Rwork0.1757 27649 -
obs0.1786 29276 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.96 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 24 227 2684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01332525
X-RAY DIFFRACTIONf_angle_d1.23533434
X-RAY DIFFRACTIONf_chiral_restr0.078357
X-RAY DIFFRACTIONf_plane_restr0.0079450
X-RAY DIFFRACTIONf_dihedral_angle_d21.3016897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.30041090.24472283X-RAY DIFFRACTION99.21
1.85-1.910.30051470.23732319X-RAY DIFFRACTION99.28
1.91-1.980.29361270.21792260X-RAY DIFFRACTION99.5
1.98-2.060.32051430.22462298X-RAY DIFFRACTION99.59
2.06-2.150.25561140.20822333X-RAY DIFFRACTION99.63
2.15-2.270.26991050.20012320X-RAY DIFFRACTION99.43
2.27-2.410.26051320.19762288X-RAY DIFFRACTION99.63
2.41-2.60.22911450.1952293X-RAY DIFFRACTION99.55
2.6-2.860.2621400.20652329X-RAY DIFFRACTION99.84
2.86-3.270.23941860.18382232X-RAY DIFFRACTION99.38
3.27-4.120.18411310.14222331X-RAY DIFFRACTION99.47
4.12-35.480.1721480.13782363X-RAY DIFFRACTION99.56

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