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- PDB-6qsh: Crystal structure of the hybrid bioinorganic complex of Pizza6S l... -

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Basic information

Entry
Database: PDB / ID: 6qsh
TitleCrystal structure of the hybrid bioinorganic complex of Pizza6S linked by the 1:2 Ce-substituted Keggin
ComponentsPizza6S
KeywordsDE NOVO PROTEIN / Artificial beta-propeller protein / computational design / polyoxometalate / POM / Pizza / polyoxometalate-protein framework / POM-protein framework / 1:2 Ce-substituted Keggin
Function / homology1:2 Ce-substituted Keggin
Function and homology information
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNoguchi, H. / Vandebroek, L. / Kamata, K. / Tame, J.R.H. / Van Meervelt, L. / Parac-Vogt, T.N. / Voet, A.R.D.
Funding support Belgium, Japan, 4items
OrganizationGrant numberCountry
G0E4717N Belgium
G0F9316N Belgium
G051917N Belgium
16H04779 Japan
CitationJournal: Chem.Commun.(Camb.) / Year: 2020
Title: Hybrid assemblies of a symmetric designer protein and polyoxometalates with matching symmetry.
Authors: Vandebroek, L. / Noguchi, H. / Kamata, K. / Tame, J.R.H. / Van Meervelt, L. / Parac-Vogt, T.N. / Voet, A.R.D.
History
DepositionFeb 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 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: Pizza6S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7123
Polymers25,7191
Non-polymers10,9932
Water37821
1
A: Pizza6S
hetero molecules

A: Pizza6S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4256
Polymers51,4392
Non-polymers21,9864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)53.367, 67.258, 69.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-402-

JGH

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Components

#1: Protein Pizza6S


Mass: 25719.295 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: Chemical ChemComp-JGH / 1:2 Ce-substituted Keggin


Mass: 5496.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CeH2O78P2W22
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.05M Magnesium acetate, 0.1M Sodium acetate, 10% (w/v) PEG8000

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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 PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→48.39 Å / Num. obs: 9133 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 6 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.146 / Net I/σ(I): 8.5
Reflection shellResolution: 2.5→2.6 Å / CC1/2: 0.802 / Rpim(I) all: 0.523 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ww9

3ww9


Resolution: 2.5→42.368 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.98
RfactorNum. reflection% reflection
Rfree0.3231 479 5.26 %
Rwork0.2582 --
obs0.2614 9102 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→42.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 206 21 1976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032369
X-RAY DIFFRACTIONf_angle_d0.4374161
X-RAY DIFFRACTIONf_dihedral_angle_d1.7321478
X-RAY DIFFRACTIONf_chiral_restr0.043330
X-RAY DIFFRACTIONf_plane_restr0.003321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.86190.39751490.35412813X-RAY DIFFRACTION100
2.8619-3.60550.32161810.25612826X-RAY DIFFRACTION100
3.6055-42.37440.29311490.22292984X-RAY DIFFRACTION100

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