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- PDB-6tje: Crystal structure of the computationally designed Cake5 protein -

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Basic information

Entry
Database: PDB / ID: 6tje
TitleCrystal structure of the computationally designed Cake5 protein
ComponentsCake5
KeywordsDE NOVO PROTEIN / Beta-propeller / computationally designed / symmetrical / repeat protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsMylemans, B. / Laier, I. / 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: Cake5
B: Cake5


Theoretical massNumber of molelcules
Total (without water)43,8102
Polymers43,8102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-17 kcal/mol
Surface area13470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.621, 66.727, 85.993
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 Cake5


Mass: 21905.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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: 2.89 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium chloride, 20% PEG3350

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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 EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.15→52.72 Å / Num. obs: 12312 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 107.16 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.033 / Rrim(I) all: 0.119 / Χ2: 0.98 / Net I/σ(I): 11.3
Reflection shellResolution: 3.15→3.37 Å / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3074 / CC1/2: 0.961 / Rpim(I) all: 0.211 / Rrim(I) all: 0.769 / Χ2: 1.17 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Cake9

Resolution: 3.15→52.72 Å / SU ML: 0.384 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.3247
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2614 629 5.11 %
Rwork0.237 11683 -
obs0.2382 12312 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.19 Å2
Refinement stepCycle: LAST / Resolution: 3.15→52.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 0 0 2397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352463
X-RAY DIFFRACTIONf_angle_d0.86573395
X-RAY DIFFRACTIONf_chiral_restr0.0557369
X-RAY DIFFRACTIONf_plane_restr0.0048461
X-RAY DIFFRACTIONf_dihedral_angle_d4.9609371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.470.40251560.31262918X-RAY DIFFRACTION98.4
3.47-3.970.32151700.262889X-RAY DIFFRACTION98.49
3.97-50.21691680.23442912X-RAY DIFFRACTION99.55
5-52.720.2441350.21772964X-RAY DIFFRACTION99.71

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