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- PDB-8r3d: Crystal structure of Pent only at pH 8.8 -

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Basic information

Entry
Database: PDB / ID: 8r3d
TitleCrystal structure of Pent only at pH 8.8
ComponentsBeta propeller
KeywordsSUGAR BINDING PROTEIN / Pentamer / beta propeller / mutivalent / synthetic construct
Function / homologyTachylectin 2 / Tachylectin 2 superfamily / Tachylectin / 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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,74610
Polymers26,6405
Non-polymers1,1065
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-22 kcal/mol
Surface area10100 Å2
Unit cell
Length a, b, c (Å)52.740, 59.131, 72.464
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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.: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.54 % / Description: Lack defined edges
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 15% PEG 10000 100 mM Tris-HCl pH 8.8

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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 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.71→45.81 Å / Num. obs: 25008 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 17.61 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.045 / Rrim(I) all: 0.112 / Net I/σ(I): 11.2
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1239 / CC1/2: 0.79 / Rpim(I) all: 0.32 / Rrim(I) all: 0.69 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→45.81 Å / SU ML: 0.1805 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.4526
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1881 1248 4.99 %
Rwork0.161 23750 -
obs0.1624 24998 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.91 Å2
Refinement stepCycle: LAST / Resolution: 1.71→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 75 258 2183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081990
X-RAY DIFFRACTIONf_angle_d0.93552705
X-RAY DIFFRACTIONf_chiral_restr0.0616280
X-RAY DIFFRACTIONf_plane_restr0.0083340
X-RAY DIFFRACTIONf_dihedral_angle_d10.791300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.780.25531500.22592596X-RAY DIFFRACTION99.93
1.78-1.860.2261280.18462592X-RAY DIFFRACTION99.96
1.86-1.960.18161300.15642631X-RAY DIFFRACTION99.96
1.96-2.080.20611270.16552619X-RAY DIFFRACTION99.96
2.08-2.240.2561480.16412590X-RAY DIFFRACTION100
2.24-2.470.20711330.16242635X-RAY DIFFRACTION99.93
2.47-2.830.17651280.1772659X-RAY DIFFRACTION99.71
2.83-3.560.20221530.15452651X-RAY DIFFRACTION99.72
3.56-45.810.14281510.14392777X-RAY DIFFRACTION99.39

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