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- PDB-6tjc: Crystal structure of the computationally designed Cake3 protein -

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Basic information

Entry
Database: PDB / ID: 6tjc
TitleCrystal structure of the computationally designed Cake3 protein
ComponentsCake3
KeywordsDE NOVO PROTEIN / Beta-propeller / computationally designed / symmetrical / repeat protein
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLaier, I. / Mylemans, B. / Voet, A.R.D. / Noguchi, H.
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: Cake3
B: Cake3
C: Cake3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,69511
Polymers39,9473
Non-polymers7488
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-49 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.541, 64.313, 106.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Cake3


Mass: 13315.628 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.05M Potassium phosphate, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→46.36 Å / Num. obs: 28542 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.02 / Rrim(I) all: 0.059 / Χ2: 0.95 / Net I/σ(I): 21.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 1793 / CC1/2: 0.957 / Rpim(I) all: 0.132 / Rrim(I) all: 0.409 / Χ2: 0.78 / % possible all: 100

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Processing

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

Resolution: 1.9→46.36 Å / SU ML: 0.1529 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6721
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2061 1432 5.03 %
Rwork0.1702 27064 -
obs0.172 28496 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.83 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 44 240 3023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842864
X-RAY DIFFRACTIONf_angle_d0.95393887
X-RAY DIFFRACTIONf_chiral_restr0.0628399
X-RAY DIFFRACTIONf_plane_restr0.0054509
X-RAY DIFFRACTIONf_dihedral_angle_d18.84381017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.970.24781190.18382679X-RAY DIFFRACTION100
1.97-2.050.23261410.17762638X-RAY DIFFRACTION100
2.05-2.140.21071360.17672690X-RAY DIFFRACTION100
2.14-2.250.21351580.16672658X-RAY DIFFRACTION100
2.25-2.390.21741570.16392662X-RAY DIFFRACTION99.89
2.39-2.580.22081470.18272703X-RAY DIFFRACTION99.82
2.58-2.840.24881200.19362698X-RAY DIFFRACTION99.96
2.84-3.250.22981470.19252716X-RAY DIFFRACTION100
3.25-4.090.18781550.15882741X-RAY DIFFRACTION99.93
4.09-46.360.17941520.15542879X-RAY DIFFRACTION99.7

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