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- PDB-6tji: Crystal structure of the computationally designed Cake10 protein -

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Basic information

Entry
Database: PDB / ID: 6tji
TitleCrystal structure of the computationally designed Cake10 protein
ComponentsCake10
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: 2.2 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: Cake10
B: Cake10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4728
Polymers79,9022
Non-polymers5706
Water1,982110
1
A: Cake10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2364
Polymers39,9511
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cake10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2364
Polymers39,9511
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.014, 63.328, 85.264
Angle α, β, γ (deg.)90.000, 90.285, 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 Cake10


Mass: 39950.844 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium Phosphate, 20% PEG3350

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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: 2.2→45.02 Å / Num. obs: 34755 / % possible obs: 99.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 47.79 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.044 / Rrim(I) all: 0.097 / Χ2: 0.84 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3008 / CC1/2: 0.678 / Rpim(I) all: 0.344 / Rrim(I) all: 0.76 / Χ2: 0.88 / % possible all: 99.7

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Processing

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

Resolution: 2.2→42.63 Å / SU ML: 0.3764 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.4621
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2605 1728 4.98 %
Rwork0.2202 33005 -
obs0.2222 34733 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.26 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5352 0 30 110 5492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515517
X-RAY DIFFRACTIONf_angle_d1.10137531
X-RAY DIFFRACTIONf_chiral_restr0.0691792
X-RAY DIFFRACTIONf_plane_restr0.0059997
X-RAY DIFFRACTIONf_dihedral_angle_d19.77641889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.3951510.33832736X-RAY DIFFRACTION99.76
2.26-2.340.37811360.30572726X-RAY DIFFRACTION99.83
2.34-2.420.33281310.28872764X-RAY DIFFRACTION100
2.42-2.520.31311670.26132703X-RAY DIFFRACTION99.9
2.52-2.630.32221620.27182727X-RAY DIFFRACTION99.69
2.63-2.770.29581330.25252756X-RAY DIFFRACTION99.76
2.77-2.950.34431130.26552759X-RAY DIFFRACTION99.48
2.95-3.170.27671570.25022735X-RAY DIFFRACTION99.62
3.17-3.490.25031330.22792743X-RAY DIFFRACTION99.55
3.49-40.25931440.21232767X-RAY DIFFRACTION99.32
4-5.030.21011540.17872759X-RAY DIFFRACTION99.28
5.03-42.630.23361470.18522830X-RAY DIFFRACTION99.27

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