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- PDB-6g6p: Crystal structure of the computationally designed Ika8 protein: c... -

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Basic information

Entry
Database: PDB / ID: 6g6p
TitleCrystal structure of the computationally designed Ika8 protein: crystal packing No.2 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: 2.4 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


Theoretical massNumber of molelcules
Total (without water)34,4221
Polymers34,4221
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.374, 127.374, 53.869
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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.66 Å3/Da / Density % sol: 66.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6 / Details: 0.1M MES pH6.0, 1.0M LiCl, 20% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→48.41 Å / Num. obs: 19765 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 0.999 / Rpim(I) all: 0.018 / Net I/σ(I): 19.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 20.4 % / Mean I/σ(I) obs: 3.3 / CC1/2: 0.91 / Rpim(I) all: 0.245 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.405 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.19
RfactorNum. reflection% reflection
Rfree0.2631 919 4.66 %
Rwork0.2115 --
obs0.2139 19742 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 0 36 2425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032445
X-RAY DIFFRACTIONf_angle_d0.5993324
X-RAY DIFFRACTIONf_dihedral_angle_d4.8781909
X-RAY DIFFRACTIONf_chiral_restr0.058395
X-RAY DIFFRACTIONf_plane_restr0.002420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.52660.35161280.2922672X-RAY DIFFRACTION100
2.5266-2.68490.37931310.29612656X-RAY DIFFRACTION100
2.6849-2.89220.32041250.29252676X-RAY DIFFRACTION100
2.8922-3.18320.31351170.26122686X-RAY DIFFRACTION100
3.1832-3.64370.26231320.22342685X-RAY DIFFRACTION100
3.6437-4.59010.24871380.17972691X-RAY DIFFRACTION100
4.5901-48.41530.23371480.1862757X-RAY DIFFRACTION100

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