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- PDB-6tjf: Crystal structure of the computationally designed Cake6 protein -

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Basic information

Entry
Database: PDB / ID: 6tjf
TitleCrystal structure of the computationally designed Cake6 protein
ComponentsCake6
KeywordsDE NOVO PROTEIN / Beta-propeller / computationally designed / symmetrical / repeat protein
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMylemans, B. / Laier, I. / 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: Cake6
B: Cake6
C: Cake6
D: Cake6
E: Cake6
F: Cake6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,84313
Polymers157,1996
Non-polymers6457
Water5,459303
1
A: Cake6
E: Cake6
F: Cake6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9687
Polymers78,5993
Non-polymers3684
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9950 Å2
ΔGint-33 kcal/mol
Surface area27580 Å2
MethodPISA
2
B: Cake6
C: Cake6
D: Cake6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8766
Polymers78,5993
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-42 kcal/mol
Surface area26910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.812, 79.670, 79.670
Angle α, β, γ (deg.)75.251, 66.137, 66.137
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Cake6


Mass: 26199.795 Da / Num. of mol.: 6
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.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium sulfate, 0.1M Tris pH 8.5, 25% PEG5000MME

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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: 2.4→57.05 Å / Num. obs: 54166 / % possible obs: 98.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 46.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.033 / Rrim(I) all: 0.062 / Χ2: 0.52 / Net I/σ(I): 8.4
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4459 / CC1/2: 0.907 / Rpim(I) all: 0.0235 / Rrim(I) all: 0.453 / Χ2: 0.61 / % possible all: 97.7

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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 crystal structure

Resolution: 2.4→57.05 Å / SU ML: 0.3249 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.3629
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2509 2811 5.19 %
Rwork0.1871 51321 -
obs0.1903 54132 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.15 Å2
Refinement stepCycle: LAST / Resolution: 2.4→57.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10927 0 42 303 11272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009611244
X-RAY DIFFRACTIONf_angle_d0.947515267
X-RAY DIFFRACTIONf_chiral_restr0.06521584
X-RAY DIFFRACTIONf_plane_restr0.00552013
X-RAY DIFFRACTIONf_dihedral_angle_d18.78983990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.32571630.21952500X-RAY DIFFRACTION97.72
2.44-2.490.36111560.23812543X-RAY DIFFRACTION97.72
2.49-2.530.35071680.24592538X-RAY DIFFRACTION97.69
2.53-2.590.32311420.24782536X-RAY DIFFRACTION98.1
2.59-2.640.31571230.25962610X-RAY DIFFRACTION97.82
2.64-2.70.35231410.24412506X-RAY DIFFRACTION98.07
2.7-2.770.31561470.23942556X-RAY DIFFRACTION98.36
2.77-2.850.30331160.24442625X-RAY DIFFRACTION98.17
2.85-2.930.32981390.22292545X-RAY DIFFRACTION98.35
2.93-3.020.271450.2292550X-RAY DIFFRACTION98.36
3.02-3.130.2791730.24292610X-RAY DIFFRACTION98.55
3.13-3.260.31931110.23322532X-RAY DIFFRACTION98.62
3.26-3.410.34491310.23122585X-RAY DIFFRACTION98.69
3.41-3.580.25731060.19452615X-RAY DIFFRACTION98.77
3.59-3.810.28221260.18062603X-RAY DIFFRACTION98.91
3.81-4.10.28321090.17592621X-RAY DIFFRACTION98.95
4.1-4.520.16991280.13722585X-RAY DIFFRACTION99.12
4.52-5.170.18861820.14172549X-RAY DIFFRACTION99.09
5.17-6.510.21051720.14072539X-RAY DIFFRACTION99.23
6.51-57.050.17121330.15582573X-RAY DIFFRACTION97.97

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