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- PDB-7alf: The dimethylated RSL - sulfonato-calix[8]arene complex, P3 form, ... -

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Basic information

Entry
Database: PDB / ID: 7alf
TitleThe dimethylated RSL - 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 / metal ion 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: 1.261 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

Downloads & links

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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)23,56910
Polymers19,6862
Non-polymers3,8848
Water6,503361
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)35,35415
Polymers29,5283
Non-polymers5,82612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7660 Å2
ΔGint-15 kcal/mol
Surface area13890 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)35,35415
Polymers29,5283
Non-polymers5,82612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area7660 Å2
ΔGint-16 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.478, 59.478, 64.720
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-337-

HOH

21A-350-

HOH

31B-332-

HOH

41B-354-

HOH

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Components

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


Mass: 9842.753 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Gene: RSP795_21825, RSP799_05830, 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


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


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


Mass: 18.015 Da / Num. of mol.: 361 / 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: 3.36 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 277.15 K / Method: batch mode / pH: 4
Details: 20 mM sodium acetate 50 mM NaCl 5 mM D-fructose 10 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: 1.26→64.72 Å / Num. obs: 68362 / % possible obs: 99 % / Redundancy: 1 % / CC1/2: 1 / Rpim(I) all: 0.28 / Rrim(I) all: 0.61 / Net I/σ(I): 16.4
Reflection shellResolution: 1.26→1.28 Å / Redundancy: 2.9 % / Num. unique obs: 3377 / CC1/2: 0.92 / % possible all: 97.1

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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: 1.261→40.303 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 2.11 / Phase error: 16.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1619 3490 5.11 %
Rwork0.1446 64809 -
obs0.1454 68299 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.77 Å2 / Biso mean: 19.6227 Å2 / Biso min: 10.01 Å2
Refinement stepCycle: final / Resolution: 1.261→40.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 252 369 2011
Biso mean--19.94 31.17 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041698
X-RAY DIFFRACTIONf_angle_d0.7962388
X-RAY DIFFRACTIONf_chiral_restr0.073228
X-RAY DIFFRACTIONf_plane_restr0.004400
X-RAY DIFFRACTIONf_dihedral_angle_d10.193536
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2612-1.27850.26921260.2405259997
1.2785-1.29670.24831630.2275251797
1.2967-1.31610.23611620.2011254998
1.3161-1.33660.22141520.1863249898
1.3366-1.35860.22851520.1837258398
1.3586-1.3820.20781600.1664257298
1.382-1.40710.19191000.1598256798
1.4071-1.43420.20221640.1538253299
1.4342-1.46350.1719940.1421264199
1.4635-1.49530.18651460.1484258399
1.4953-1.53010.14831330.1373262299
1.5301-1.56830.16961540.1408258099
1.5683-1.61070.19081520.1378257999
1.6107-1.65810.13981360.1404262399
1.6581-1.71170.1951600.1393255999
1.7117-1.77280.1956900.13832649100
1.7728-1.84380.16281540.14192590100
1.8438-1.92770.14811650.1373258499
1.9277-2.02940.15211240.14262605100
2.0294-2.15650.15471360.144264699
2.1565-2.3230.17771540.14722586100
2.323-2.55670.17751120.15052651100
2.5567-2.92660.14921240.14542652100
2.9266-3.68680.14791270.13712637100
3.6868-40.3030.12911500.13072605100

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