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- PDB-8r3c: Cocrystal form II of the Pent - sulfonato-calix[8]arene complex -

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Basic information

Entry
Database: PDB / ID: 8r3c
TitleCocrystal form II 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: 1.58 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

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Assembly

Deposited unit
A: Beta propeller
B: Beta propeller
C: Beta propeller
D: Beta propeller
E: Beta propeller
F: Beta propeller
G: Beta propeller
H: Beta propeller
I: Beta propeller
J: Beta propeller
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,98121
Polymers53,28010
Non-polymers3,70211
Water6,197344
1
A: Beta propeller
B: Beta propeller
C: Beta propeller
D: Beta propeller
E: Beta propeller
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,23511
Polymers26,6405
Non-polymers2,5966
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-24 kcal/mol
Surface area10010 Å2
MethodPISA
2
F: Beta propeller
G: Beta propeller
H: Beta propeller
I: Beta propeller
J: Beta propeller
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,74610
Polymers26,6405
Non-polymers1,1065
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-24 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.975, 52.055, 69.284
Angle α, β, γ (deg.)90.000, 104.370, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 5327.980 Da / Num. of mol.: 10 / 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: 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.: 10 / 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-EVB / sulfonato-calix[8]arene


Mass: 1489.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H48O32S8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 1.93 Å3/Da / Density % sol: 36.3 % / Description: Distorted ellipsoid
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 15% PEG 10000 50 mM MgCl2

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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: Mar 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98013 Å / Relative weight: 1
ReflectionResolution: 1.58→57.13 Å / Num. obs: 55808 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 24.96 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Net I/σ(I): 14
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 7 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2779 / CC1/2: 0.934 / Rpim(I) all: 0.25 / Rrim(I) all: 0.664 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→57.13 Å / SU ML: 0.1948 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.5521
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2224 2710 4.86 %
Rwork0.1797 53061 -
obs0.1818 55771 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.67 Å2
Refinement stepCycle: LAST / Resolution: 1.58→57.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3700 0 246 344 4290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834084
X-RAY DIFFRACTIONf_angle_d0.9885578
X-RAY DIFFRACTIONf_chiral_restr0.0622560
X-RAY DIFFRACTIONf_plane_restr0.0073760
X-RAY DIFFRACTIONf_dihedral_angle_d13.06711434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.610.3771340.30662784X-RAY DIFFRACTION99.83
1.61-1.640.37651520.28062759X-RAY DIFFRACTION99.83
1.64-1.670.33681640.27092743X-RAY DIFFRACTION99.76
1.67-1.710.3061250.23922794X-RAY DIFFRACTION99.9
1.71-1.750.30141420.21942791X-RAY DIFFRACTION99.97
1.75-1.790.27021340.20932803X-RAY DIFFRACTION99.97
1.79-1.840.25561610.19992776X-RAY DIFFRACTION99.86
1.84-1.90.23231450.19172753X-RAY DIFFRACTION99.86
1.9-1.960.27021480.19132773X-RAY DIFFRACTION99.97
1.96-2.030.27121170.19472832X-RAY DIFFRACTION99.93
2.03-2.110.22341310.18952797X-RAY DIFFRACTION99.93
2.11-2.20.27891440.19912790X-RAY DIFFRACTION99.9
2.2-2.320.24071370.19922792X-RAY DIFFRACTION99.76
2.32-2.470.26891340.21042820X-RAY DIFFRACTION99.73
2.47-2.660.29151400.21022782X-RAY DIFFRACTION99.8
2.66-2.920.22621530.20242811X-RAY DIFFRACTION99.9
2.92-3.350.241830.17412758X-RAY DIFFRACTION99.73
3.35-4.210.13991150.13742863X-RAY DIFFRACTION99.77
4.22-57.130.16451510.15082840X-RAY DIFFRACTION97.87

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