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- PDB-8p2u: Crystal structure of S6BE with Silicotungstic Acid (STA) polyoxom... -

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Basic information

Entry
Database: PDB / ID: 8p2u
TitleCrystal structure of S6BE with Silicotungstic Acid (STA) polyoxometalate
ComponentsS6BE
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 / Resolution: 1.4 Å
AuthorsWouters, S.M.L. / Kamata, K. / Vandebroek, L.
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: Crystal structure of S6BE with Silicotungstic Acid (STA) polyoxometalate
Authors: Wouters, S.M.L. / Kamata, K. / Takahashi, K. / Vandebroek, L. / Parac-Vogt, T.N. / Tame, J.R.H. / Voet, A.R.D.
History
DepositionMay 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S6BE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3332
Polymers30,4581
Non-polymers2,8741
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10830 Å2
Unit cell
Length a, b, c (Å)34.976, 43.244, 44.069
Angle α, β, γ (deg.)63.28, 90.00, 66.15
Int Tables number1
Space group name H-MP1

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Components

#1: Protein S6BE


Mass: 30458.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#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.: 212 / 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: 1.74 Å3/Da / Density % sol: 29.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 5 / Details: 1.5 M Sodium malonate, pH 5.0

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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: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→38.38 Å / Num. obs: 61953 / % possible obs: 94.9 % / Redundancy: 1.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.06 / Rrim(I) all: 0.084 / Χ2: 0.96 / Net I/σ(I): 10
Reflection shellResolution: 1.4→1.42 Å / % possible obs: 93.9 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.134 / Num. measured all: 3386 / Num. unique obs: 1866 / CC1/2: 0.944 / Rpim(I) all: 0.134 / Rrim(I) all: 0.189 / Χ2: 0.41 / Net I/σ(I) obs: 5.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→38.38 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 2.08 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 3132 5.06 %
Rwork0.1792 --
obs0.1809 61953 76.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→38.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 53 212 2338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072289
X-RAY DIFFRACTIONf_angle_d1.4463342
X-RAY DIFFRACTIONf_dihedral_angle_d10.321813
X-RAY DIFFRACTIONf_chiral_restr0.094337
X-RAY DIFFRACTIONf_plane_restr0.013390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.27541130.24352550X-RAY DIFFRACTION74
1.42-1.450.25271770.24162510X-RAY DIFFRACTION72
1.45-1.470.32211360.2312340X-RAY DIFFRACTION68
1.47-1.50.31221610.25092632X-RAY DIFFRACTION75
1.5-1.530.29141260.23682574X-RAY DIFFRACTION73
1.53-1.560.29681370.23142446X-RAY DIFFRACTION71
1.56-1.590.24911060.22012617X-RAY DIFFRACTION73
1.59-1.630.26121450.21992645X-RAY DIFFRACTION77
1.63-1.670.30021190.21772713X-RAY DIFFRACTION76
1.67-1.710.2761330.20462709X-RAY DIFFRACTION77
1.71-1.760.20351120.19592643X-RAY DIFFRACTION73
1.76-1.820.22481220.18862646X-RAY DIFFRACTION76
1.82-1.890.18151340.18182720X-RAY DIFFRACTION78
1.89-1.960.23931630.15872605X-RAY DIFFRACTION75
1.96-2.050.19831550.14832693X-RAY DIFFRACTION78
2.05-2.160.15351600.15052858X-RAY DIFFRACTION81
2.16-2.290.19791750.15492752X-RAY DIFFRACTION80
2.29-2.470.19541480.16792603X-RAY DIFFRACTION76
2.47-2.720.18051720.16742922X-RAY DIFFRACTION82
2.72-3.110.19411480.16442716X-RAY DIFFRACTION79
3.11-3.920.20421590.15632973X-RAY DIFFRACTION84
3.92-38.380.18151310.17582954X-RAY DIFFRACTION84

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