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- PDB-7zqg: Crystal structure of Pizza6-KSH-TSH with Silicotungstic Acid (STA... -

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Basic information

Entry
Database: PDB / ID: 7zqg
TitleCrystal structure of Pizza6-KSH-TSH with Silicotungstic Acid (STA) polyoxometalate
ComponentsPizza6-KSH-TSH
KeywordsUNKNOWN FUNCTION / beta propeller / synthetic / designer / polyoxometalate / STA / co-crystal / silicotungstic acid
Function / homologyKeggin (STA)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsWouters, S.M.L. / Kamata, K. / Takahashi, K. / Vandebroek, L. / Parac-Vogt, T.N. / Tame, J.R.H. / Voet, A.R.D.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1S89918N Belgium
Research Foundation - Flanders (FWO)G0F9316N Belgium
Research Foundation - Flanders (FWO)G051917N Belgium
CitationJournal: To be published
Title: Mutational study of a symmetry matched protein-polyoxometalate interface
Authors: Wouters, S. / Kamata, K. / Takahashi, K. / Vandebroek, L. / Parac-Vogt, T.N. / Tame, J.R.H. / Voet, A.R.D.
History
DepositionApr 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Feb 7, 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

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Assembly

Deposited unit
A: Pizza6-KSH-TSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7472
Polymers25,8731
Non-polymers2,8741
Water1,982110
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 area10210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.092, 70.092, 85.055
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

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Components

#1: Protein Pizza6-KSH-TSH


Mass: 25872.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-SIW / Keggin (STA)


Mass: 2874.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O40SiW12 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.02 Å3/Da / Density % sol: 39.07 % / Mosaicity: 0.09 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magnesium acetate, 20%(w/v) PEG 3350

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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 EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→49.56 Å / Num. obs: 20312 / % possible obs: 100 % / Redundancy: 25.6 % / Biso Wilson estimate: 20.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.041 / Rrim(I) all: 0.205 / Net I/σ(I): 16.8 / Num. measured all: 519534 / Scaling rejects: 1270
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.8427.21.3843238611900.9480.2691.415.1100
9-49.5618.90.07740422140.9990.0170.07843.399.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.25 Å49.56 Å
Translation5.25 Å49.56 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WW9

3ww9


Resolution: 1.8→49.56 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2109 1811 4.83 %
Rwork0.1804 35693 -
obs0.1819 20312 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.73 Å2 / Biso mean: 21.7724 Å2 / Biso min: 7.18 Å2
Refinement stepCycle: final / Resolution: 1.8→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 106 111 1979
Biso mean--42.17 26.74 -
Num. residues----247
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.850.2641350.208227232858
1.85-1.90.2371440.192227452889
1.9-1.960.2581470.191827272874
1.96-2.030.21381290.165227702899
2.03-2.120.24811710.173727402911
2.12-2.210.21951280.179927372865
2.21-2.330.27311150.184227672882
2.33-2.480.27061540.181227252879
2.48-2.670.21721430.188427632906
2.67-2.930.19781270.182727492876
2.93-3.360.21941290.175727632892
3.36-4.230.18091440.177827452889
4.23-49.560.1741450.177627392884
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3078-0.1988-0.23531.15060.2780.4171-0.2334-0.1842-0.22150.73260.16140.13560.219-0.0299-0.09070.21870.03580.04930.09050.01810.19969.3699-24.17287.724
21.1039-0.1258-0.661.07670.49451.0291-0.1414-0.17240.08380.20650.08090.1333-0.0333-0.0819-0.09070.13360.0318-0.00070.0895-0.0060.12448.8556-7.30144.8071
30.6877-0.615-0.00811.6859-0.29371.0498-0.0280.00470.0032-0.050.0086-0.1201-0.04060.0911-0.00650.0852-0.000300.0861-0.00610.142816.6221-17.6088-7.5967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 195 through 251 )A195 - 251
2X-RAY DIFFRACTION2chain 'A' and (resid 2 through 82 )A2 - 82
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 194 )A83 - 194

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