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- PDB-9hrz: The RSL-R6 - pctx complex, H3 form -

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Basic information

Entry
Database: PDB / ID: 9hrz
TitleThe RSL-R6 - pctx complex, H3 form
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / Complex
Function / homologyFucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / : / beta-D-fructopyranose / Fucose-binding lectin protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsWren, C.P. / Mockler, N.M. / Crowley, P.B.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/RC/2275_P2 Ireland
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Protein Recognition and Assembly by a Phosphocavitand.
Authors: Wren, C.P. / Flood, R.J. / Mockler, N.M. / Savko, M. / Malinska, M. / Shi, Q. / Crowley, P.B.
History
DepositionDec 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4515
Polymers9,8181
Non-polymers1,6334
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.569, 43.569, 122.997
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-34-

ARG

21A-219-

HOH

31A-290-

HOH

41A-293-

HOH

51A-299-

HOH

61A-307-

HOH

71A-309-

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 / Mutation: K25R, K34R, K83R
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 (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.: 2 / 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
#3: Chemical ChemComp-A1IXG / phosphated-cyclotrixylohydroquinoylene


Mass: 636.417 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H27O12P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.13 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.8 M ammonium sulfate, 0.1 M sodium acetate pH 5.6

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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: Oct 26, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.49→18.65 Å / Num. obs: 14063 / % possible obs: 99.6 % / Redundancy: 10.3 % / Biso Wilson estimate: 10.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.071 / Rrim(I) all: 0.054 / Net I/σ(I): 25.6
Reflection shellResolution: 1.49→1.52 Å / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 4873 / CC1/2: 0.983 / Rpim(I) all: 0.106 / Rrim(I) all: 0.297 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→18.65 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2028 699 4.98 %
Rwork0.1715 --
obs0.1729 14030 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→18.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms694 0 108 109 911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006853
X-RAY DIFFRACTIONf_angle_d1.3011209
X-RAY DIFFRACTIONf_dihedral_angle_d12.64323
X-RAY DIFFRACTIONf_chiral_restr0.085116
X-RAY DIFFRACTIONf_plane_restr0.023201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.610.25151240.19562644X-RAY DIFFRACTION98
1.61-1.770.20631500.1762663X-RAY DIFFRACTION100
1.77-2.030.21841520.18232668X-RAY DIFFRACTION100
2.03-2.550.20671370.17882672X-RAY DIFFRACTION100
2.55-18.650.18391360.15792684X-RAY DIFFRACTION100

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