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- PDB-6z5z: The RSL-R6 - sulfonato-calix[8]arene complex, P213 form, TRIS-HCl... -

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Basic information

Entry
Database: PDB / ID: 6z5z
TitleThe RSL-R6 - sulfonato-calix[8]arene complex, P213 form, TRIS-HCl pH 8.5
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: 1.124 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
DepositionMay 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6674
Polymers9,8181
Non-polymers1,8503
Water2,270126
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)35,00212
Polymers29,4533
Non-polymers5,5499
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area6610 Å2
ΔGint-11 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.820, 63.820, 63.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-292-

HOH

21A-306-

HOH

31A-325-

HOH

41A-326-

HOH

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Components

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


Mass: 9817.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RSL-R6 is an RSL mutant with all three lysines mutated to arginines (K25R, K34R, K83R).
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1
#2: 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
#3: Sugar ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.19 Å3/Da / Density % sol: 31.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M TRIS-HCl pH 8.5, 1.6 M Ammonium sulfate, 0.2 M Lithium sulfate, 0.04 M sulfonato-calix[8]arene, 0.005 M D-fructose

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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: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.12→45.13 Å / Num. obs: 33221 / % possible obs: 100 % / Redundancy: 36.9 % / CC1/2: 0.998 / Rpim(I) all: 0.027 / Rrim(I) all: 0.168 / Net I/σ(I): 19.3
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 23.1 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1632 / CC1/2: 0.772 / Rpim(I) all: 0.461 / Rrim(I) all: 2.236 / % 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: 1.124→45.128 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1752 1673 5.04 %
Rwork0.1573 31545 -
obs0.1582 33218 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.42 Å2 / Biso mean: 14.3383 Å2 / Biso min: 5.62 Å2
Refinement stepCycle: final / Resolution: 1.124→45.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms679 0 120 126 925
Biso mean--15.02 29.29 -
Num. residues----88
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005859
X-RAY DIFFRACTIONf_angle_d0.8371211
X-RAY DIFFRACTIONf_chiral_restr0.075118
X-RAY DIFFRACTIONf_plane_restr0.007206
X-RAY DIFFRACTIONf_dihedral_angle_d10.023270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.124-1.15710.21100.1912614
1.1571-1.19440.21771510.17332585
1.1944-1.23710.18881250.16452620
1.2371-1.28660.16581450.1622602
1.2866-1.34520.16761360.15542595
1.3452-1.41610.16641470.15932606
1.4161-1.50480.18131490.16582613
1.5048-1.6210.16681220.14912643
1.621-1.78420.18021530.15362611
1.7842-2.04240.17341690.14562617
2.0424-2.57310.19131160.15872680
2.5731-45.1280.16121500.15572759

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