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- PDB-7pr5: Cocrystal of an RSL-N23H and sulfonato-thiacalix[4]arene - zinc c... -

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Basic information

Entry
Database: PDB / ID: 7pr5
TitleCocrystal of an RSL-N23H and sulfonato-thiacalix[4]arene - zinc complex
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / calixarene / molecular glue / metal binding / synthetic receptor / b-propeller / thiacalixarene
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Lipocalin - #190 / Fucose-specific lectin / Fungal fucose-specific lectin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
sulfonato-thiacalix[4]arene / beta-D-fructopyranose / Fucose-binding lectin protein
Similarity search - Component
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsFlood, R.J. / Ramberg, K. / Guagnini, F. / Crowley, P.B.
Funding support Ireland, 3items
OrganizationGrant numberCountry
Science Foundation Ireland12/RC/2275_P2 Ireland
Science Foundation Ireland13/CDA/2168 Ireland
Irish Research CouncilGOIPD/2019/513 Ireland
CitationJournal: Cryst.Growth Des. / Year: 2022
Title: Protein Frameworks with Thiacalixarene and Zinc.
Authors: Flood, R.J. / Ramberg, K.O. / Mengel, D.B. / Guagnini, F. / Crowley, P.B.
History
DepositionSep 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Fucose-binding lectin protein
D: Fucose-binding lectin protein
E: Fucose-binding lectin protein
F: Fucose-binding lectin protein
G: Fucose-binding lectin protein
H: Fucose-binding lectin protein
I: Fucose-binding lectin protein
J: Fucose-binding lectin protein
K: Fucose-binding lectin protein
L: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,60244
Polymers117,09112
Non-polymers5,51032
Water15,457858
1
A: Fucose-binding lectin protein
B: Fucose-binding lectin protein
C: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,48511
Polymers29,2733
Non-polymers1,2128
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-18 kcal/mol
Surface area11300 Å2
MethodPISA
2
D: Fucose-binding lectin protein
E: Fucose-binding lectin protein
F: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,41910
Polymers29,2733
Non-polymers1,1467
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-17 kcal/mol
Surface area11330 Å2
MethodPISA
3
G: Fucose-binding lectin protein
H: Fucose-binding lectin protein
I: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,39711
Polymers29,2733
Non-polymers1,1248
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-20 kcal/mol
Surface area11650 Å2
MethodPISA
4
J: Fucose-binding lectin protein
K: Fucose-binding lectin protein
L: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,30112
Polymers29,2733
Non-polymers2,0299
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-36 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.370, 129.400, 130.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 35 molecules ABCDEFGHIJKL

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


Mass: 9757.606 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: E7Z57_08365, HXP36_18875, RSP795_21825, RSP822_19650, RUN39_v1_50103
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1
#2: Sugar...
ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 23 / 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

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Non-polymers , 4 types, 867 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-80M / sulfonato-thiacalix[4]arene


Mass: 816.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H16O16S8 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 858 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 16% PEG 3350, 200 mM tri-Sodium citrate pH 8.3, 60 mM zinc acetate

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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: 1.94→46.84 Å / Num. obs: 85149 / % possible obs: 99.4 % / Redundancy: 13.6 % / Biso Wilson estimate: 32.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.036 / Rrim(I) all: 0.132 / Net I/σ(I): 14.8 / Num. measured all: 1155816
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.94-1.9912.81.8487373157730.5820.5231.9231.492.4
8.66-46.8411.20.03812259109410.0120.0449.199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.76 Å46.84 Å
Translation3.76 Å46.84 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BT9

2bt9


Resolution: 1.94→46.84 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 4252 5 %
Rwork0.1833 80780 -
obs0.1853 85032 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.6 Å2 / Biso mean: 33.5422 Å2 / Biso min: 17.46 Å2
Refinement stepCycle: final / Resolution: 1.94→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8209 0 337 858 9404
Biso mean--40.77 38.32 -
Num. residues----1071
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-1.960.42331140.37342180229482
1.96-1.980.38851420.346426972839100
1.98-2.010.32311400.297826542794100
2.01-2.030.34561410.271126852826100
2.03-2.060.25831410.25326692810100
2.06-2.090.30271410.238626842825100
2.09-2.120.31991400.230526692809100
2.12-2.150.32961420.232126882830100
2.15-2.180.26851410.230426772818100
2.18-2.220.25821400.211126642804100
2.22-2.250.24661430.211527172860100
2.25-2.30.25051400.211226642804100
2.3-2.340.25081410.215226802821100
2.34-2.390.29051420.2226942836100
2.39-2.440.2491420.223226892831100
2.44-2.50.26451430.226427172860100
2.5-2.560.28831410.213826882829100
2.56-2.630.28271410.192426842825100
2.63-2.70.25061430.187227162859100
2.7-2.790.25841420.186626942836100
2.79-2.890.24231420.185427012843100
2.89-3.010.24281430.182527132856100
3.01-3.140.21021430.187527102853100
3.14-3.310.2031430.167727192862100
3.31-3.520.18771440.157227362880100
3.52-3.790.18551430.161427282871100
3.79-4.170.18511460.149827742920100
4.17-4.770.16111460.129227612907100
4.77-6.010.161470.144727952942100
6.01-46.840.22161550.183929333088100

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