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- PDB-6qsf: Crystal structure of Pizza6S in the presence of Keggin (STA) -

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Basic information

Entry
Database: PDB / ID: 6qsf
TitleCrystal structure of Pizza6S in the presence of Keggin (STA)
ComponentsPizza6S
KeywordsDE NOVO PROTEIN / Artificial beta-propeller protein / computational design / polyoxometalate / POM / Pizza / polyoxometalate-protein framework / POM-protein framework / Keggin structure / STA
Function / homologyKeggin (STA)
Function and homology information
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
B: Pizza6S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1874
Polymers51,4392
Non-polymers5,7482
Water4,197233
1
A: Pizza6S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5932
Polymers25,7191
Non-polymers2,8741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pizza6S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5932
Polymers25,7191
Non-polymers2,8741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.244, 69.777, 62.675
Angle α, β, γ (deg.)90.00, 104.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pizza6S


Mass: 25719.295 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-SIW / Keggin (STA)


Mass: 2874.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O40SiW12 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.03 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.5M Sodium malonate pH6.0

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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 S 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: 1.5→47.64 Å / Num. obs: 65621 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 16.6 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.072 / Net I/σ(I): 9.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.3 / Rpim(I) all: 0.575 / % possible all: 99.5

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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: 1.5→47.639 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.27
RfactorNum. reflection% reflection
Rfree0.2378 3244 4.95 %
Rwork0.2241 --
obs0.2248 65586 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→47.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3537 0 106 233 3876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123941
X-RAY DIFFRACTIONf_angle_d1.1985749
X-RAY DIFFRACTIONf_dihedral_angle_d9.651377
X-RAY DIFFRACTIONf_chiral_restr0.078667
X-RAY DIFFRACTIONf_plane_restr0.008686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52240.26031500.30182667X-RAY DIFFRACTION99
1.5224-1.54620.27851580.28522715X-RAY DIFFRACTION100
1.5462-1.57160.2891420.27222677X-RAY DIFFRACTION100
1.5716-1.59870.2991340.26942684X-RAY DIFFRACTION100
1.5987-1.62770.24141450.25172685X-RAY DIFFRACTION100
1.6277-1.65910.30051330.25052714X-RAY DIFFRACTION100
1.6591-1.69290.29351330.24852739X-RAY DIFFRACTION100
1.6929-1.72970.26731360.24892688X-RAY DIFFRACTION100
1.7297-1.770.29331420.24942735X-RAY DIFFRACTION100
1.77-1.81420.27141350.24582695X-RAY DIFFRACTION100
1.8142-1.86330.27481410.24032691X-RAY DIFFRACTION100
1.8633-1.91810.26321440.24832716X-RAY DIFFRACTION100
1.9181-1.980.24711270.23712721X-RAY DIFFRACTION100
1.98-2.05080.23141460.23792720X-RAY DIFFRACTION100
2.0508-2.13290.27891390.24482693X-RAY DIFFRACTION100
2.1329-2.230.22871210.24492747X-RAY DIFFRACTION100
2.23-2.34760.26421520.23182701X-RAY DIFFRACTION100
2.3476-2.49460.24451410.2242684X-RAY DIFFRACTION100
2.4946-2.68720.23221550.21362721X-RAY DIFFRACTION100
2.6872-2.95760.22091480.21712705X-RAY DIFFRACTION100
2.9576-3.38550.25461300.21112723X-RAY DIFFRACTION100
3.3855-4.26490.20741390.20172753X-RAY DIFFRACTION100
4.2649-47.66330.17951530.17792768X-RAY DIFFRACTION99

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