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- PDB-7zph: Crystal structure of Pizza6-TNK-RSH with Silicotungstic Acid (STA... -

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Basic information

Entry
Database: PDB / ID: 7zph
TitleCrystal structure of Pizza6-TNK-RSH with Silicotungstic Acid (STA) polyoxometalate
ComponentsPizza6-TNK-RSH
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: 1.66 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 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 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-TNK-RSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8852
Polymers26,0111
Non-polymers2,8741
Water2,126118
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 area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.190, 70.190, 85.662
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-486-

HOH

21A-501-

HOH

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Components

#1: Protein Pizza6-TNK-RSH


Mass: 26010.844 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.: 118 / 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: 2.03 Å3/Da / Density % sol: 39.35 % / Mosaicity: 0.08 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1 M MES pH 6.5, 0.6 M tri-Na citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.66→42.94 Å / Num. obs: 25993 / % possible obs: 100 % / Redundancy: 23.8 % / Biso Wilson estimate: 20.94 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.028 / Rrim(I) all: 0.138 / Net I/σ(I): 23 / Num. measured all: 617509 / Scaling rejects: 4331
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
1.66-1.6913.40.7831674512520.8780.2230.8164.499.8
9.09-42.9413.10.10926902060.9820.0330.11430.498.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.3 Å42.94 Å
Translation5.3 Å42.94 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: 1.66→42.94 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 2376 4.92 %
Rwork0.2042 45892 -
obs0.2052 25993 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.37 Å2 / Biso mean: 24.8999 Å2 / Biso min: 11.04 Å2
Refinement stepCycle: final / Resolution: 1.66→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 159 122 1999
Biso mean--34.75 30.13 -
Num. residues----243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.66-1.690.41651330.28772647278099
1.69-1.730.26271290.27427212850100
1.73-1.770.32051290.275627172846100
1.77-1.820.29311470.241727002847100
1.82-1.860.31351520.246726942846100
1.86-1.920.28351390.224826912830100
1.92-1.980.25231510.208327132864100
1.98-2.050.25161200.19327092829100
2.05-2.130.23111540.196726912845100
2.13-2.230.25571380.21126872825100
2.23-2.350.20591610.190427002861100
2.35-2.50.2661300.21126962826100
2.5-2.690.2111150.208227372852100
2.69-2.960.26371310.222627092840100
2.96-3.390.23911250.187827052830100
3.39-4.270.18731900.189226632853100
4.27-42.940.17181320.186827122844100
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)
10.1299-0.067-0.00750.2283-0.19250.3217-0.0193-0.0304-0.1083-0.057-0.10440.1110.1111-0.2025-0.00480.1161-0.00650.0150.162-0.00330.10954.069710.489419.9144
20.94530.68740.18170.5767-0.06090.52140.0810.0890.2390.0397-0.04540.1262-0.0937-0.1011-0.00710.08860.00590.01410.1120.00620.125316.059816.874511.9737
30.0843-0.0802-0.23110.88670.17480.64290.167-0.3763-0.16140.0256-0.1086-0.17970.03070.15240.17980.1201-0.0434-0.04480.2560.05110.176425.036810.287427.3677
40.65980.2868-0.02240.34810.07590.15410.0891-0.3721-0.06680.1431-0.1165-0.1365-0.03380.1329-0.10880.1935-0.0804-0.02440.26920.0280.127610.87327.328931.157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 39 )A4 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 132 )A40 - 132
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 207 )A133 - 207
4X-RAY DIFFRACTION4chain 'A' and (resid 208 through 251 )A208 - 251

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