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- PDB-8r3b: Cocrystal form I of the Pent - sulfonato-calix[8]arene complex -

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Basic information

Entry
Database: PDB / ID: 8r3b
TitleCocrystal form I of the Pent - sulfonato-calix[8]arene complex
ComponentsBeta propellerBeta-propeller
KeywordsSUGAR BINDING PROTEIN / Complex / beta propeller / mutivalent / synthetic construct
Function / homologyTachylectin 2 / Tachylectin 2 superfamily / Tachylectin / sulfonato-calix[8]arene / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Beta propeller
Function and homology information
Biological speciesEnterobacteria phage L1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsFlood, R.J. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/RC/2275_P2 Ireland
Citation
Journal: Biomacromolecules / Year: 2024
Title: Multivalent Calixarene Complexation of a Designed Pentameric Lectin.
Authors: Flood, R.J. / Cerofolini, L. / Fragai, M. / Crowley, P.B.
#1: Journal: Cell / Year: 2016
Title: De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints.
Authors: Smock, R.G. / Yadid, I. / Dym, O. / Clarke, J. / Tawfik, D.S.
History
DepositionNov 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta propeller
B: Beta propeller
E: Beta propeller
D: Beta propeller
C: Beta propeller
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,23511
Polymers26,6405
Non-polymers2,5966
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9810 Å2
ΔGint-28 kcal/mol
Surface area10260 Å2
Unit cell
Length a, b, c (Å)52.084, 52.084, 177.488
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-225-

HOH

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Components

#1: Protein/peptide
Beta propeller / Beta-propeller


Mass: 5327.980 Da / Num. of mol.: 5 / Mutation: N33K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage L1 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A140UHM9
#2: Chemical ChemComp-EVB / sulfonato-calix[8]arene


Mass: 1489.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H48O32S8 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE / N-Acetylglucosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.19 Å3/Da / Density % sol: 43.94 % / Description: Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% PEG 1000 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98013 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98013 Å / Relative weight: 1
ReflectionResolution: 1.66→49.98 Å / Num. obs: 30163 / % possible obs: 100 % / Redundancy: 23.9 % / Biso Wilson estimate: 23.26 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.02 / Rrim(I) all: 0.096 / Net I/σ(I): 19.8
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 24.7 % / Rmerge(I) obs: 1.57 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1490 / CC1/2: 0.85 / Rpim(I) all: 0.32 / Rrim(I) all: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.20.1_4487refinement
autoPROCdata processing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→49.98 Å / SU ML: 0.2621 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.6127
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2379 1460 4.84 %
Rwork0.1922 28695 -
obs0.1944 30155 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.47 Å2
Refinement stepCycle: LAST / Resolution: 1.66→49.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 171 157 2178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612094
X-RAY DIFFRACTIONf_angle_d0.84622873
X-RAY DIFFRACTIONf_chiral_restr0.0564280
X-RAY DIFFRACTIONf_plane_restr0.0068420
X-RAY DIFFRACTIONf_dihedral_angle_d10.9801324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.720.44851510.38562809X-RAY DIFFRACTION99.97
1.72-1.780.3281200.30362797X-RAY DIFFRACTION99.93
1.78-1.870.27551470.23072823X-RAY DIFFRACTION99.97
1.87-1.960.25231530.20352799X-RAY DIFFRACTION100
1.96-2.090.27831370.19662863X-RAY DIFFRACTION99.97
2.09-2.250.27651470.18692812X-RAY DIFFRACTION99.93
2.25-2.470.22131490.18052864X-RAY DIFFRACTION100
2.47-2.830.25461560.20852872X-RAY DIFFRACTION100
2.83-3.570.2071510.18522916X-RAY DIFFRACTION100
3.57-49.980.20841490.16563140X-RAY DIFFRACTION99.88

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