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- PDB-6g6o: Crystal structure of the computationally designed Ika8 protein: c... -

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Basic information

Entry
Database: PDB / ID: 6g6o
TitleCrystal structure of the computationally designed Ika8 protein: crystal packing No.1 in P63
ComponentsIka8
KeywordsDE NOVO PROTEIN / Artificial protein / WD40 proteins
Function / homologyYVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsNoguchi, H. / Addy, C. / Simoncini, D. / Van Meervelt, L. / Schiex, T. / Zhang, K.Y.J. / Tame, J.R.H. / Voet, A.R.D.
Funding support Belgium, Japan, 2items
OrganizationGrant numberCountry
G0E4717N, G0F9316N, G051917N Belgium
Japan Science and Technology16H04779 Japan
CitationJournal: IUCrJ / Year: 2019
Title: Computational design of symmetrical eight-bladed beta-propeller proteins.
Authors: Noguchi, H. / Addy, C. / Simoncini, D. / Wouters, S. / Mylemans, B. / Van Meervelt, L. / Schiex, T. / Zhang, K.Y.J. / Tame, J.R.H. / Voet, A.R.D.
History
DepositionApr 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Ika8
B: Ika8
C: Ika8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6337
Polymers103,2653
Non-polymers3684
Water3,927218
1
A: Ika8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6063
Polymers34,4221
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ika8


Theoretical massNumber of molelcules
Total (without water)34,4221
Polymers34,4221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ika8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6063
Polymers34,4221
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)218.609, 218.609, 53.569
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Ika8


Mass: 34421.574 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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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: 3.58 Å3/Da / Density % sol: 65.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8
Details: 0.1M Tris-HCl pH8.0, 0.2M CaCl2, 15% Glycerol, 16% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→46.62 Å / Num. obs: 90235 / % possible obs: 98 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rpim(I) all: 0.019 / Net I/σ(I): 27.9
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4.2 % / CC1/2: 0.88 / Rpim(I) all: 0.145 / % possible all: 85.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→46.62 Å / Cross valid method: FREE R-VALUE / σ(F): 7.91 / Phase error: 34.76
RfactorNum. reflection% reflection
Rfree0.2529 4404 4.88 %
Rwork0.2281 --
obs0.2383 90223 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7167 0 24 218 7409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027343
X-RAY DIFFRACTIONf_angle_d0.499973
X-RAY DIFFRACTIONf_dihedral_angle_d4.7365739
X-RAY DIFFRACTIONf_chiral_restr0.0491186
X-RAY DIFFRACTIONf_plane_restr0.0021263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0502-2.08550.31241620.27913666X-RAY DIFFRACTION80
2.0855-2.12350.31372080.27343837X-RAY DIFFRACTION84
2.1235-2.16430.29762110.27293949X-RAY DIFFRACTION87
2.1643-2.20850.30172230.27854290X-RAY DIFFRACTION93
2.2085-2.25650.32812180.27344330X-RAY DIFFRACTION95
2.2565-2.3090.32042280.27954359X-RAY DIFFRACTION95
2.309-2.36670.33031960.28834405X-RAY DIFFRACTION96
2.3667-2.43070.30921920.27864437X-RAY DIFFRACTION96
2.4307-2.50220.28882140.27874322X-RAY DIFFRACTION95
2.5022-2.5830.2912350.2684375X-RAY DIFFRACTION95
2.583-2.67530.30582000.26144432X-RAY DIFFRACTION96
2.6753-2.78240.28762160.26584349X-RAY DIFFRACTION95
2.7824-2.9090.28812600.25724353X-RAY DIFFRACTION94
2.909-3.06240.3062680.24284352X-RAY DIFFRACTION94
3.0624-3.25420.24482260.22984396X-RAY DIFFRACTION95
3.2542-3.50540.23272190.21944420X-RAY DIFFRACTION95
3.5054-3.8580.25572350.21214409X-RAY DIFFRACTION95
3.858-4.41580.2112110.19394415X-RAY DIFFRACTION95
4.4158-5.5620.20762550.1864392X-RAY DIFFRACTION93
5.562-46.63340.26381960.25614354X-RAY DIFFRACTION90

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