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- PDB-7zpz: Crystal structure of Pizza6-TSR-TSH with Silicotungstic Acid (STA... -

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Basic information

Entry
Database: PDB / ID: 7zpz
TitleCrystal structure of Pizza6-TSR-TSH with Silicotungstic Acid (STA) polyoxometalate
ComponentsPizza6-TSR-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: 1.57 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-TSR-TSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7202
Polymers25,8461
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 area10210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.826, 69.826, 85.549
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-488-

HOH

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Components

#1: Protein Pizza6-TSR-TSH


Mass: 25845.541 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: 2.02 Å3/Da / Density % sol: 39.03 % / Mosaicity: 0.09 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 0.0085 M Cobalt chloride, 0.085 M MES pH 6.5, 1.53 M Ammonium sulfate, 15% (v/v) Glycerol
PH range: pH 6.5

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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 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.57→42.77 Å / Num. obs: 30288 / % possible obs: 100 % / Redundancy: 25.9 % / Biso Wilson estimate: 16.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.035 / Rrim(I) all: 0.181 / Net I/σ(I): 16.5 / Num. measured all: 784827 / Scaling rejects: 640
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
1.57-1.624.51.463654914910.8720.2981.4913.9100
8.6-42.7719.60.06846782390.9990.0150.0746.799.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.25 Å42.76 Å
Translation5.25 Å42.76 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: 1.57→42.76 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 2870 5.08 %
Rwork0.1893 53606 -
obs0.1906 30288 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.72 Å2 / Biso mean: 20.6314 Å2 / Biso min: 8.08 Å2
Refinement stepCycle: final / Resolution: 1.57→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 159 120 2052
Biso mean--23.77 27.35 -
Num. residues----250
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.57-1.60.26781610.245427112872
1.6-1.630.30571500.237126642814
1.63-1.660.29351280.231826782806
1.66-1.690.28431360.224327182854
1.69-1.730.28671530.211926672820
1.73-1.770.27211290.225326692798
1.77-1.810.25461540.203226632817
1.81-1.860.26131410.196427032844
1.86-1.920.21451560.191226392795
1.92-1.980.2411620.180726942856
1.98-2.050.26011450.17826772822
2.05-2.130.20931530.183226592812
2.13-2.230.23241360.191826552791
2.23-2.350.20721490.180627062855
2.35-2.490.23741500.193226642814
2.49-2.680.21271180.179427102828
2.68-2.950.21361350.180426692804
2.95-3.380.20791390.175626872826
3.38-4.260.18621520.192126642816
4.26-42.760.17371230.180227092832
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)
10.1992-0.0776-0.15470.62060.04660.3448-0.093-0.174-0.02340.26870.09410.1472-0.1176-0.0572-0.00990.18510.04220.00250.13310.00640.11058.7772-7.6435.8386
20.263-0.2844-0.03650.5229-0.3510.6941-0.02450.03020.0336-0.01640.0209-0.0353-0.07090.0318-0.0010.0883-0.0073-0.01010.0669-0.00480.095315.7814-13.7095-9.0773
30.6454-0.2905-0.09670.7034-0.15320.3827-0.08760.0511-0.14220.16230.08090.02970.0715-0.03220.01640.12830.02670.01570.05910.01530.120211.5683-24.83884.3424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 79 )A5 - 79
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 169 )A80 - 169
3X-RAY DIFFRACTION3chain 'A' and (resid 170 through 254 )A170 - 254

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