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- PDB-7zq2: Crystal structure of Pizza6-RSH-TSH with Silicotungstic Acid (STA... -

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Basic information

Entry
Database: PDB / ID: 7zq2
TitleCrystal structure of Pizza6-RSH-TSH with Silicotungstic Acid (STA) polyoxometalate
ComponentsPizza6-RSH-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: 1.6 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-RSH-TSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4535
Polymers25,9571
Non-polymers11,4974
Water1,820101
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 area10740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.245, 61.893, 69.953
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pizza6-RSH-TSH


Mass: 25956.670 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.: 4 / Source method: obtained synthetically / Formula: O40SiW12 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.05 Å3/Da / Density % sol: 40.1 % / Mosaicity: 0.06 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 4.6 / Details: 0.1 M Sodium acetate pH 4.6, 2.0 M Sodium chloride

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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: 1.6→49.24 Å / Num. obs: 28917 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 15.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.036 / Rrim(I) all: 0.13 / Net I/σ(I): 18.1 / Num. measured all: 367931 / Scaling rejects: 398
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
1.6-1.638.20.6941148813990.8770.2530.7413.699.4
8.76-49.249.60.05720662150.9950.0190.0652.998.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.25 Å40.27 Å
Translation5.25 Å40.27 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: 1.6→40.27 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2267 2785 5.12 %
Rwork0.1998 51638 -
obs0.2012 28917 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.77 Å2 / Biso mean: 20.6328 Å2 / Biso min: 10.26 Å2
Refinement stepCycle: final / Resolution: 1.6→40.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 318 102 2141
Biso mean--28.63 25.28 -
Num. residues----241
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.630.32831550.28372536269199
1.63-1.660.26431280.253125742702100
1.66-1.690.2471000.215126172717100
1.69-1.720.23051510.213826022753100
1.72-1.760.25081260.20826022728100
1.76-1.80.22541440.208225702714100
1.8-1.850.24341400.210425512691100
1.85-1.90.23161490.201426062755100
1.9-1.950.20811540.206525622716100
1.95-2.020.22381410.192125622703100
2.02-2.090.24021280.201626352763100
2.09-2.170.24211310.220625442675100
2.17-2.270.28221670.22325812748100
2.27-2.390.25171500.211825882738100
2.39-2.540.28331010.225125972698100
2.54-2.740.22981580.200725882746100
2.74-3.010.21871440.21125762720100
3.01-3.450.2011440.188425782722100
3.45-4.340.21271330.190125882721100
4.34-40.270.19081410.163225812722100
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)
10.34680.03590.51410.11560.10670.7993-0.1002-0.1575-0.1443-0.0079-0.0270.0150.017-0.0858-0.28140.0652-0.0010.02960.07080.02460.122121.6061-0.936417.1565
20.06030.08370.04680.13910.14770.4177-0.0769-0.1485-0.08590.1810.1562-0.05660.00040.14150.04630.08990.0192-0.01340.12680.02390.169634.4395-0.34911.5068
30.01520.0146-0.05010.31860.34860.69180.03990.0309-0.0966-0.05020.0345-0.2067-0.05350.30930.10230.0791-0.00790.00820.1386-0.01110.215634.8731.4661-1.3694
40.13840.02110.10250.0151-0.00930.1262-0.00060.22350.02780.0161-0.0798-0.1415-0.10850.0546-0.02490.1059-0.02060.0020.12730.0020.136321.49132.6972-7.4581
50.12490.234-0.22210.5237-0.30830.5701-0.08070.08150.0078-0.22260.00870.10920.1288-0.3859-0.10370.1141-0.0204-0.0020.1355-0.01830.10512.46461.6025.3341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 160 through 207 )A160 - 207
2X-RAY DIFFRACTION2chain 'A' and (resid 208 through 251 )A208 - 251
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 51 )A1 - 51
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 91 )A52 - 91
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 159 )A92 - 159

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