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- PDB-7alg: The RSLex - sulfonato-calix[8]arene complex, P3 form, acetate pH 4.0 -

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Basic information

Entry
Database: PDB / ID: 7alg
TitleThe RSLex - sulfonato-calix[8]arene complex, P3 form, acetate pH 4.0
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / calixarene / protein framework / cage / crystal engineering / molecular glue / synthetic receptor / macrocycle / biomaterial
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / beta-D-fructopyranose / sulfonato-calix[8]arene / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.452 Å
AuthorsRamberg, K. / Engilberge, S. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Facile Fabrication of Protein-Macrocycle Frameworks.
Authors: Ramberg, K.O. / Engilberge, S. / Skorek, T. / Crowley, P.B.
History
DepositionOct 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fucose-binding lectin protein
B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,50510
Polymers19,6212
Non-polymers3,8848
Water6,287349
1
A: Fucose-binding lectin protein
hetero molecules

A: Fucose-binding lectin protein
hetero molecules

A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,25815
Polymers29,4323
Non-polymers5,82612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7690 Å2
ΔGint-13 kcal/mol
Surface area13510 Å2
MethodPISA
2
B: Fucose-binding lectin protein
hetero molecules

B: Fucose-binding lectin protein
hetero molecules

B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,25815
Polymers29,4323
Non-polymers5,82612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area7690 Å2
ΔGint-14 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.680, 59.680, 64.284
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

21A-357-

HOH

31B-327-

HOH

41B-349-

HOH

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Components

#1: Protein Fucose-binding lectin protein / Putative fucose-binding lectin protein


Mass: 9810.710 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S4TLR1
#2: Chemical ChemComp-EVB / sulfonato-calix[8]arene


Mass: 1489.481 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C56H48O32S8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar
ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose / Fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DFrupbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructopyranoseCOMMON NAMEGMML 1.0
b-D-FrupIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 3.37 Å3/Da / Density meas: 59 Mg/m3
Crystal growTemperature: 277.15 K / Method: batch mode / pH: 4
Details: 20 mM acetate 50 mM NaCl 5 mM D-fructose 15 mM sclx8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.45→27.294 Å / Num. obs: 45237 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 1 / Rpim(I) all: 0.03 / Rrim(I) all: 0.068 / Net I/σ(I): 15.7
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2252 / CC1/2: 0.915 / Rpim(I) all: 0.377 / Rrim(I) all: 0.835 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BT9

2bt9


Resolution: 1.452→27.294 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 2.09 / Phase error: 17.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1677 2302 5.09 %
Rwork0.1438 42883 -
obs0.1449 45185 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.75 Å2 / Biso mean: 23.7098 Å2 / Biso min: 12.8 Å2
Refinement stepCycle: final / Resolution: 1.452→27.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 252 352 1990
Biso mean--24.61 35.29 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051696
X-RAY DIFFRACTIONf_angle_d0.7582380
X-RAY DIFFRACTIONf_chiral_restr0.072226
X-RAY DIFFRACTIONf_plane_restr0.004400
X-RAY DIFFRACTIONf_dihedral_angle_d10.082536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.452-1.48360.28481520.23552694100
1.4836-1.51810.24161720.20272638100
1.5181-1.55610.20881300.17622681100
1.5561-1.59810.21361190.16212722100
1.5981-1.64510.20821160.15782701100
1.6451-1.69820.1782010.15122638100
1.6982-1.75890.17681280.14152701100
1.7589-1.82930.20951420.15152670100
1.8293-1.91260.19851230.14682666100
1.9126-2.01340.15081310.1472687100
2.0134-2.13950.18442000.144265699
2.1395-2.30460.1681710.14672641100
2.3046-2.53640.15491620.1482645100
2.5364-2.9030.1537880.14592743100
2.903-3.65610.17441200.13412709100
3.6561-27.2940.13491470.12862691100

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