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- PDB-9hry: The MK-RSL - pctx complex, P41212 form -

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Basic information

Entry
Database: PDB / ID: 9hry
TitleThe MK-RSL - pctx complex, P41212 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: 1.5 Å
AuthorsWren, C.W. / 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,81430
Polymers59,4416
Non-polymers6,37324
Water11,349630
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)32,90715
Polymers29,7213
Non-polymers3,18612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-133 kcal/mol
Surface area12520 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)32,90715
Polymers29,7213
Non-polymers3,18612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-133 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.158, 112.158, 99.312
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11C-273-

HOH

21C-290-

HOH

31E-283-

HOH

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Components

#1: Protein
Fucose-binding lectin protein


Mass: 9906.859 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Gene: E7Z57_08365, HF909_06975, LBW55_09125, 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.: 12 / 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.: 6 / Source method: obtained synthetically / Formula: C27H27O12P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 2.52 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 20% PEG 3350, 0.2 M zinc acetate, 0.1 M Imidazole pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 7, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.5→61.97 Å / Num. obs: 102148 / % possible obs: 100 % / Redundancy: 26.7 % / Biso Wilson estimate: 17.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.027 / Rrim(I) all: 0.142 / Net I/σ(I): 17.4
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 21 % / Rmerge(I) obs: 1.582 / Mean I/σ(I) obs: 2 / Num. unique obs: 5025 / CC1/2: 0.613 / Rpim(I) all: 0.347 / Rrim(I) all: 1.621 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→61.97 Å / SU ML: 0.1666 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6273
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1988 5041 4.94 %
Rwork0.1758 97092 -
obs0.1769 102133 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.09 Å2
Refinement stepCycle: LAST / Resolution: 1.5→61.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4194 0 402 630 5226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01634759
X-RAY DIFFRACTIONf_angle_d1.58936641
X-RAY DIFFRACTIONf_chiral_restr0.1206691
X-RAY DIFFRACTIONf_plane_restr0.0101950
X-RAY DIFFRACTIONf_dihedral_angle_d10.93991697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.510.30171660.2773168X-RAY DIFFRACTION99.85
1.51-1.530.28681480.25623212X-RAY DIFFRACTION100
1.53-1.550.28041570.24413199X-RAY DIFFRACTION100
1.55-1.570.27711540.2413212X-RAY DIFFRACTION100
1.57-1.590.25981700.23273185X-RAY DIFFRACTION100
1.59-1.610.24591810.22383173X-RAY DIFFRACTION100
1.61-1.630.25621770.20893176X-RAY DIFFRACTION100
1.63-1.660.25631790.20733218X-RAY DIFFRACTION100
1.66-1.680.23811750.20243204X-RAY DIFFRACTION100
1.68-1.710.22191590.2023183X-RAY DIFFRACTION100
1.71-1.740.22641630.20123240X-RAY DIFFRACTION100
1.74-1.770.2311630.2053183X-RAY DIFFRACTION99.94
1.77-1.810.22451530.19723239X-RAY DIFFRACTION99.97
1.81-1.840.23351790.19993203X-RAY DIFFRACTION100
1.84-1.880.21051620.18723210X-RAY DIFFRACTION100
1.88-1.930.22161720.1893224X-RAY DIFFRACTION100
1.93-1.980.21851720.1763186X-RAY DIFFRACTION100
1.98-2.030.1921580.18223250X-RAY DIFFRACTION100
2.03-2.090.19911570.17143222X-RAY DIFFRACTION100
2.09-2.160.21751970.17523223X-RAY DIFFRACTION100
2.16-2.230.17111740.17273233X-RAY DIFFRACTION100
2.23-2.320.20161670.1733231X-RAY DIFFRACTION100
2.32-2.430.19871730.16723240X-RAY DIFFRACTION100
2.43-2.560.22471530.17763277X-RAY DIFFRACTION100
2.56-2.720.18391670.16893247X-RAY DIFFRACTION100
2.72-2.930.20241430.17543310X-RAY DIFFRACTION100
2.93-3.220.18361830.17153281X-RAY DIFFRACTION100
3.22-3.690.18041860.1593293X-RAY DIFFRACTION99.97
3.69-4.650.15241630.13553361X-RAY DIFFRACTION100
4.65-61.970.15061900.14813509X-RAY DIFFRACTION99.76

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