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- PDB-9fro: Crystal structure of Pent - p-sulfonatocalix[6]arene complex -

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Basic information

Entry
Database: PDB / ID: 9fro
TitleCrystal structure of Pent - p-sulfonatocalix[6]arene complex
ComponentsBeta propeller
KeywordsSUGAR BINDING PROTEIN / Complex / Beta-propeller / Lectin / Pentamer
Function / homologyTachylectin 2 / Tachylectin 2 superfamily / Tachylectin / p-sulfonatocalix[6]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: 1.71 Å
AuthorsFlood, R.J. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/RC/2275_P2 Ireland
Citation
Journal: ACS Macro Lett / Year: 2024
Title: A Macrocycle-Mediated Protein Cage.
Authors: Flood, R.J. / Thureau, A. / Crowley, P.B.
#1: Journal: Biomacromolecules / Year: 2024
Title: Multivalent Calixarene Complexation of a Designed Pentameric Lectin.
Authors: Flood, R.J. / Cerofolini, L. / Fragai, M. / Crowley, P.B.
History
DepositionJun 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)31,96913
Polymers26,6405
Non-polymers5,3298
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.570, 92.689, 112.376
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11D-104-

FWQ

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Components

#1: Protein/peptide
Beta propeller


Mass: 5327.980 Da / Num. of mol.: 5
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: 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


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 4 / 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
#3: Chemical
ChemComp-FWQ / p-sulfonatocalix[6]arene


Mass: 1111.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H30O24S6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.78 Å3/Da / Density % sol: 55 % / Description: bipyramidal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.2 M ammonium sulfate 0.1 M sodium malonate; pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.71→56.19 Å / Num. obs: 31640 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 21.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.037 / Rrim(I) all: 0.129 / Net I/σ(I): 12.4
Reflection shellResolution: 1.712→1.742 Å / Rmerge(I) obs: 1.438 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1593 / CC1/2: 0.779 / Rpim(I) all: 0.439 / Rrim(I) all: 1.505 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→56.19 Å / SU ML: 0.2117 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.0286
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2157 1541 4.87 %
Rwork0.1897 30081 -
obs0.191 31622 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.78 Å2
Refinement stepCycle: LAST / Resolution: 1.71→56.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 348 135 2341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552295
X-RAY DIFFRACTIONf_angle_d0.77483198
X-RAY DIFFRACTIONf_chiral_restr0.0529276
X-RAY DIFFRACTIONf_plane_restr0.0052580
X-RAY DIFFRACTIONf_dihedral_angle_d8.5562507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.770.32051590.29192669X-RAY DIFFRACTION99.96
1.77-1.830.26821360.22242703X-RAY DIFFRACTION99.93
1.83-1.90.241410.19692709X-RAY DIFFRACTION100
1.9-1.990.24671420.19232711X-RAY DIFFRACTION99.93
1.99-2.10.21861340.18482686X-RAY DIFFRACTION99.82
2.1-2.230.20061420.18312730X-RAY DIFFRACTION99.93
2.23-2.40.24181280.18522725X-RAY DIFFRACTION99.93
2.4-2.640.25651170.21032750X-RAY DIFFRACTION99.93
2.64-3.020.23841270.21882762X-RAY DIFFRACTION99.97
3.02-3.810.19271590.17722762X-RAY DIFFRACTION99.97
3.81-56.190.191560.16972874X-RAY DIFFRACTION99.84

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