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- PDB-6qse: Crystal structure of Pizza6S in the presence of Anderson-Evans (TEW) -

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Basic information

Entry
Database: PDB / ID: 6qse
TitleCrystal structure of Pizza6S in the presence of Anderson-Evans (TEW)
ComponentsPizza6S
KeywordsDE NOVO PROTEIN / Artificial beta-propeller protein / computational design / polyoxometalate / POM / Pizza / polyoxometalate-protein framework / POM-protein framework / Anderson-Evans / TEW
Function / homology6-tungstotellurate(VI)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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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)27,3342
Polymers25,7191
Non-polymers1,6151
Water2,180121
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 area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.420, 56.469, 69.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O24TeW6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH7.0, 22%(w/v) PEG6000

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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: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→43.84 Å / Num. obs: 17194 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rpim(I) all: 0.043 / Net I/σ(I): 15.9
Reflection shellResolution: 1.9→1.94 Å / Mean I/σ(I) obs: 3.5 / CC1/2: 0.884 / Rpim(I) all: 0.397

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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: 1.9→43.836 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 851 4.96 %
Rwork0.2009 --
obs0.2031 17146 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→43.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 31 121 1930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021985
X-RAY DIFFRACTIONf_angle_d1.0063018
X-RAY DIFFRACTIONf_dihedral_angle_d9.916656
X-RAY DIFFRACTIONf_chiral_restr0.051319
X-RAY DIFFRACTIONf_plane_restr0.005331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.01910.2651160.21542679X-RAY DIFFRACTION100
2.0191-2.1750.25451660.21842652X-RAY DIFFRACTION100
2.175-2.39380.26511580.19862653X-RAY DIFFRACTION100
2.3938-2.74020.2971430.21712706X-RAY DIFFRACTION100
2.7402-3.45210.22071340.20552725X-RAY DIFFRACTION100
3.4521-43.84750.23461340.18762880X-RAY DIFFRACTION100

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