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- PDB-7ov7: The hybrid cage formed between Pizza6-S and Cu(II)-substituted tr... -

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Basic information

Entry
Database: PDB / ID: 7ov7
TitleThe hybrid cage formed between Pizza6-S and Cu(II)-substituted trilacunary Keggin
ComponentsPizza6-S
KeywordsBIOSYNTHETIC PROTEIN / Designer protein / protein design / POM / Polyoxometalate / hybrid / cage / Cu / Keggin
Function / homologyCOPPER (II) ION / : / Trilacunary Keggin
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVandebroek, L. / Noguchi, H. / Anyushin, A. / Van Meervelt, L. / Voet, A.R.D. / Parac-Vogt, T.N.
Funding support Belgium, 4items
OrganizationGrant numberCountry
KU LeuvenPDM/20/093 Belgium
Research Foundation - Flanders (FWO)G0E4717N Belgium
Research Foundation - Flanders (FWO)G0F9316N Belgium
Research Foundation - Flanders (FWO)G051917N Belgium
CitationJournal: Cryst.Growth Des. / Year: 2022
Title: Hierarchical Self-Assembly of a Supramolecular Protein-Metal Cage Encapsulating a Polyoxometalate Guest
Authors: Vandebroek, L. / Noguchi, H. / Anyushin, A. / Van Meervelt, L. / Voet, A.R.D. / Parac-Vogt, T.N.
History
DepositionJun 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pizza6-S
B: Pizza6-S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,51316
Polymers51,4392
Non-polymers5,07514
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-56 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.792, 74.150, 79.733
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

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Components

#1: Protein Pizza6-S


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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PW9 / Trilacunary Keggin


Mass: 2229.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O34PW9 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 1.89 Å3/Da / Density % sol: 34.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 0.1M MES, 25% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→49.213 Å / Num. obs: 69759 / % possible obs: 99.9 % / Redundancy: 9.1 % / CC1/2: 0.998 / Net I/σ(I): 13.6
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2151 / CC1/2: 0.888 / Rpim(I) all: 0.262 / Rrim(I) all: 0.823

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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: 3WW9

3ww9


Resolution: 1.8→49.213 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2873 3424 4.91 %
Rwork0.2322 66335 -
obs0.2347 69759 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.02 Å2 / Biso mean: 30.8563 Å2 / Biso min: 12.19 Å2
Refinement stepCycle: final / Resolution: 1.8→49.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 188 265 3981
Biso mean--41.08 32.64 -
Num. residues----499
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.82570.38441300.35279899
1.8257-1.8530.4321740.3315270199
1.853-1.88190.35971430.33072765100
1.8819-1.91280.41241580.3326275199
1.9128-1.94580.35021490.3042765100
1.9458-1.98120.38441570.28722733100
1.9812-2.01930.30791520.28052738100
2.0193-2.06050.33081590.25762722100
2.0605-2.10530.30661420.26442777100
2.1053-2.15430.28381100.27022819100
2.1543-2.20810.3221220.24542753100
2.2081-2.26780.29311580.25872763100
2.2678-2.33460.34951510.26412750100
2.3346-2.40990.2881470.26942764100
2.4099-2.4960.24471100.25682786100
2.496-2.5960.24051270.23242807100
2.596-2.71410.29961640.2362748100
2.7141-2.85720.29511900.24152719100
2.8572-3.03620.28421400.24222763100
3.0362-3.27060.2521250.22382790100
3.2706-3.59960.29711100.20432781100
3.5996-4.12030.26141290.19942805100
4.1203-5.19020.21781230.17132785100
5.1902-49.2130.26661540.21342752100

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