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- PDB-6tjd: Crystal structure of the computationally designed Cake4 protein -

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Basic information

Entry
Database: PDB / ID: 6tjd
TitleCrystal structure of the computationally designed Cake4 protein
ComponentsCake4
KeywordsDE NOVO PROTEIN / Beta-propeller / computationally designed / symmetrical / repeat protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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: Cake4
B: Cake4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4574
Polymers35,2212
Non-polymers2362
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-32 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.913, 65.758, 71.205
Angle α, β, γ (deg.)90.000, 91.045, 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 Cake4


Mass: 17610.350 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)
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER 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: 2.1→48.31 Å / Num. obs: 18944 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 34.13 Å2 / CC1/2: 0.953 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Χ2: 0.93 / Net I/σ(I): 1.1
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 7 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1561 / CC1/2: 0.953 / Rpim(I) all: 0.186 / Rrim(I) all: 0.497 / Χ2: 0.94 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Cake8 model

Resolution: 2.1→35.6 Å / SU ML: 0.243 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.5972
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2193 894 4.73 %
Rwork0.1764 17996 -
obs0.1786 18890 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.43 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 0 16 175 2625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022518
X-RAY DIFFRACTIONf_angle_d0.44283423
X-RAY DIFFRACTIONf_chiral_restr0.047356
X-RAY DIFFRACTIONf_plane_restr0.0035450
X-RAY DIFFRACTIONf_dihedral_angle_d19.6001895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.230.29341360.2332992X-RAY DIFFRACTION99.46
2.23-2.40.28931570.20912962X-RAY DIFFRACTION99.55
2.4-2.650.2551400.20822989X-RAY DIFFRACTION99.78
2.65-3.030.26371650.20812978X-RAY DIFFRACTION99.9
3.03-3.810.24991500.17363009X-RAY DIFFRACTION99.94
3.81-35.60.15141460.14393066X-RAY DIFFRACTION99.91

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