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- PDB-6tjb: Crystal structure of the computationally designed Cake2 protein -

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Basic information

Entry
Database: PDB / ID: 6tjb
TitleCrystal structure of the computationally designed Cake2 protein
ComponentsCake2
KeywordsDE NOVO PROTEIN / Beta-propeller / computationally designed / symmetrical / repeat protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Cake2
B: Cake2
C: Cake2
D: Cake2
E: Cake2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1976
Polymers45,1055
Non-polymers921
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-50 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.888, 69.188, 82.871
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Cake2


Mass: 9020.912 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.4M potassium nitrate, 26% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→48.82 Å / Num. obs: 18200 / % possible obs: 100 % / Observed criterion σ(F): 1.34 / Redundancy: 13.3 % / Biso Wilson estimate: 43.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.042 / Rrim(I) all: 0.154 / Χ2: 0.98 / Net I/σ(I): 12.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.443 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1744 / CC1/2: 0.82 / Rpim(I) all: 0.402 / Rrim(I) all: 1.499 / Χ2: 0.96 / % possible all: 100

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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: Computational model

Resolution: 2.3→48.82 Å / SU ML: 0.3034 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2589 909 5.01 %
Rwork0.2114 17232 -
obs0.2136 18141 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.57 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 0 6 110 2853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00372809
X-RAY DIFFRACTIONf_angle_d0.97693811
X-RAY DIFFRACTIONf_chiral_restr0.0612396
X-RAY DIFFRACTIONf_plane_restr0.0037503
X-RAY DIFFRACTIONf_dihedral_angle_d21.7078998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.31131360.27742811X-RAY DIFFRACTION99.97
2.44-2.630.31081910.26282792X-RAY DIFFRACTION99.97
2.63-2.90.3271580.26262828X-RAY DIFFRACTION100
2.9-3.320.27951560.24722853X-RAY DIFFRACTION99.97
3.32-4.180.25011360.19642909X-RAY DIFFRACTION99.97
4.18-48.820.20461320.17313039X-RAY DIFFRACTION99.69

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