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- PDB-7zcj: Crystal structure of Pizza6-TNH-TSH with Silicotungstic Acid (STA... -

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Basic information

Entry
Database: PDB / ID: 7zcj
TitleCrystal structure of Pizza6-TNH-TSH with Silicotungstic Acid (STA) polyoxometalate
ComponentsPizza6-TNH-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: 1.56 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
DepositionMar 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 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-TNH-TSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7442
Polymers25,8691
Non-polymers2,8741
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.181, 69.181, 131.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-511-

HOH

21A-534-

HOH

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Components

#1: Protein Pizza6-TNH-TSH


Mass: 25869.473 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.: 152 / 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: 3.05 Å3/Da / Density % sol: 59.67 % / Mosaicity: 0.08 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M Magnesium chloride, 0.1 M MES pH 6.5, 30% (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.56→47.73 Å / Num. obs: 46485 / % possible obs: 100 % / Redundancy: 24.8 % / Biso Wilson estimate: 16.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.019 / Rrim(I) all: 0.096 / Net I/σ(I): 27.7 / Num. measured all: 1154947 / Scaling rejects: 1
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
1.56-1.5923.60.4765374722760.9830.0990.4868.1100
8.54-47.7320.20.06274203670.9990.0130.06364.799.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.82 Å47.73 Å
Translation5.82 Å47.73 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: 1.56→47.73 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1827 2271 4.89 %
Rwork0.1616 44128 -
obs0.1626 46399 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.24 Å2 / Biso mean: 27.5227 Å2 / Biso min: 12.9 Å2
Refinement stepCycle: final / Resolution: 1.56→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 106 159 2172
Biso mean--18.79 34.08 -
Num. residues----251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.56-1.590.16221430.127427212864
1.59-1.630.14231290.122727162845
1.63-1.670.12841320.109727052837
1.67-1.720.14441500.115427042854
1.72-1.770.15091190.130827382857
1.77-1.820.15691260.126527362862
1.82-1.890.18311420.14827162858
1.89-1.970.16291530.155227072860
1.97-2.050.17111530.14327212874
2.06-2.160.16961480.158527612909
2.16-2.30.18871340.163727352869
2.3-2.480.17341470.163827632910
2.48-2.730.20511350.162527712906
2.73-3.120.21511440.187427962940
3.12-3.930.19511470.181828462993
3.93-47.730.18511690.166529923161
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)
10.53240.4856-0.35950.4714-0.37790.3194-0.05680.2255-0.0949-0.09070.0113-0.07630.05050.0246-0.00060.17480.02640.020.2452-0.01620.18720.51963.9371-12.7517
21.616-0.46810.44670.9873-0.16170.15240.05130.43650.0525-0.2269-0.0447-0.05070.03770.0659-0.00210.16130.00250.010.25310.02950.134612.703215.3351-15.4729
31.2036-0.49710.32190.9844-0.15860.29380.14750.1772-0.1796-0.260.03410.13720.1640.01310.02710.22630.001-0.05920.203-0.03240.1924-0.23843.655-15.8781
40.849-0.1555-0.04861.0141-0.60760.39560.05470.1958-0.3619-0.23170.06140.01110.18590.0982-0.00410.27530.0158-0.03270.2103-0.06960.225413.0198-5.4389-12.8279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 34 )A2 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 118 )A35 - 118
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 202 )A119 - 202
4X-RAY DIFFRACTION4chain 'A' and (resid 203 through 252 )A203 - 252

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