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- PDB-6y7p: The complex between the eight-bladed symmetrical designer protein... -

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Basic information

Entry
Database: PDB / ID: 6y7p
TitleThe complex between the eight-bladed symmetrical designer protein Tako8 and 1:2 zirconium(IV) Wells-Dawson (ZrWD)
ComponentsTako8
KeywordsDE NOVO PROTEIN / Designer protein / polyoxometalate / POM / ZrWD / hybrid / framework
Function / homologyW-Zr-cluster
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVandebroek, L. / Noguchi, H. / Parac-Vogt, T.N. / Van Meervelt, L. / Voet, A.R.D.
CitationJournal: Cryst.Growth Des. / Year: 2021
Title: Shape and Size Complementarity-Induced Formation of Supramolecular Protein Assemblies with Metal-Oxo Clusters
Authors: Vandebroek, L. / Noguchi, H. / Kamata, K. / Tame, J.R.H. / Parac-Vogt, T.N. / Voet, A.R.D.
History
DepositionMar 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tako8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0505
Polymers35,0241
Non-polymers17,0264
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.347, 72.799, 54.288
Angle α, β, γ (deg.)90.000, 120.380, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tako8


Mass: 35024.230 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-ZRW / W-Zr-cluster


Mass: 4256.431 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O61P2W17Zr / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M sodium acetate pH 4.5, 3.1M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→46.834 Å / Num. obs: 70938 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.058 / Rrim(I) all: 0.106 / Net I/σ(I): 10.8
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1977 / CC1/2: 0.81 / Rpim(I) all: 0.459 / Rrim(I) all: 0.863

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Processing

Software
NameVersionClassification
PHENIX1.15.2refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6g6m

6g6m


Resolution: 1.75→46.834 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.63
RfactorNum. reflection% reflection
Rfree0.2149 3344 4.71 %
Rwork0.1778 --
obs0.1796 70938 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.94 Å2 / Biso mean: 19.338 Å2 / Biso min: 8.72 Å2
Refinement stepCycle: final / Resolution: 1.75→46.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2410 0 329 313 3052
Biso mean--34.54 24.94 -
Num. residues----318
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7501-1.77510.40671620.3494274099
1.7751-1.80160.31351730.3238285899
1.8016-1.82970.33081620.284272499
1.8297-1.85970.31651260.2899294399
1.8597-1.89180.21061040.2414277399
1.8918-1.92620.25411420.2262279599
1.9262-1.96320.24841360.2105288199
1.9632-2.00330.27451620.2112271199
2.0033-2.04690.23071200.2094282799
2.0469-2.09450.30151030.19293199
2.0945-2.14690.25471180.1803282199
2.1469-2.20490.24151340.1836280899
2.2049-2.26980.26311160.167281999
2.2698-2.34310.20751460.1682281699
2.3431-2.42680.20481990.1838274399
2.4268-2.5240.27481270.1755281699
2.524-2.63880.16731440.1652279899
2.6388-2.77790.24871480.1818280399
2.7779-2.95190.20661080.1776290999
2.9519-3.17980.17821140.1652282599
3.1798-3.49970.1821790.13592759100
3.4997-4.00590.14331500.12942838100
4.0059-5.04610.17161340.13222856100
5.0461-46.8340.22021370.1963280099

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