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- PDB-6y7o: The complex between the eight-bladed symmetrical designer protein... -

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Basic information

Entry
Database: PDB / ID: 6y7o
TitleThe complex between the eight-bladed symmetrical designer protein Tako8 and the silicotungstic acid Keggin (STA)
ComponentsTako8
KeywordsDE NOVO PROTEIN / Designer protein / polyoxometalate / POM / STA / hybrid / framework
Function / homologyKeggin (STA)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: 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: Tako8
B: Tako8
C: Tako8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,18217
Polymers104,9443
Non-polymers40,23814
Water1,15364
1
A: Tako8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1008
Polymers34,9811
Non-polymers20,1197
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tako8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6044
Polymers34,9811
Non-polymers8,6223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tako8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4785
Polymers34,9811
Non-polymers11,4974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.554, 133.505, 81.753
Angle α, β, γ (deg.)90.000, 125.270, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-406-

SIW

21B-402-

SIW

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Components

#1: Protein Tako8


Mass: 34981.203 Da / Num. of mol.: 3
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.: 14 / Source method: obtained synthetically / Formula: O40SiW12 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.01 Å3/Da / Density % sol: 38.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5 / 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: Diamond / Beamline: I04-1 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.3→47.28 Å / Num. obs: 36727 / % possible obs: 100 % / Redundancy: 9.8 % / CC1/2: 0.989 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.09 / Rrim(I) all: 0.201 / Net I/σ(I): 8.3
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3590 / CC1/2: 0.762 / Rpim(I) all: 0.679

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6g6m

6g6m


Resolution: 2.3→47.2 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.49
RfactorNum. reflection% reflection
Rfree0.2933 1912 5.21 %
Rwork0.2411 --
obs0.2439 36701 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.18 Å2 / Biso mean: 38.6316 Å2 / Biso min: 20.81 Å2
Refinement stepCycle: final / Resolution: 2.3→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7222 0 1060 65 8347
Biso mean--51.28 33.3 -
Num. residues----949
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3-2.35760.37571020.29132490
2.3576-2.42130.4411350.30552533
2.4213-2.49250.3371270.30692432
2.4925-2.5730.36951670.29412495
2.573-2.66490.35221330.28022431
2.6649-2.77160.37421360.28762459
2.7716-2.89780.30971430.272522
2.8978-3.05050.30471420.25812467
3.0505-3.24160.30241730.24242427
3.2416-3.49180.2871260.24432520
3.4918-3.84310.2581350.22092453
3.8431-4.39880.28571620.22272462
4.3988-5.54070.29581030.19462550
5.5407-47.20.22411280.2282548

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