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- PDB-9kx8: Mistletoe Lectin I from Viscum album complexed with epimer form o... -

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Basic information

Entry
Database: PDB / ID: 9kx8
TitleMistletoe Lectin I from Viscum album complexed with epimer form of lactose
Components(Beta-galactoside-specific lectin 1 chain ...) x 2
KeywordsPLANT PROTEIN / Mistletoe / Lectin / MLI
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / carbohydrate binding / negative regulation of translation
Similarity search - Function
Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins
Similarity search - Domain/homology
GLYCINE / Beta-galactoside-specific lectin 1
Similarity search - Component
Biological speciesViscum album (European mistletoe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsSaeed, A. / Betzel, C. / Brognaro, H. / Rajaiah Prabhu, P. / Alves Franca, B. / Khaliq, B. / Mehmood, S. / Akrem, A.
Funding support Pakistan, 1items
OrganizationGrant numberCountry
Other governmentIRSIP Pakistan
CitationJournal: To Be Published
Title: Mistletoe Lectin I from Viscum album complexed with epimer form of lactose
Authors: Saeed, A. / Betzel, C. / Brognaro, H. / Rajaiah Prabhu, P. / Alves Franca, B. / Khaliq, B. / Mehmood, S. / Akrem, A.
History
DepositionDec 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 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: Beta-galactoside-specific lectin 1 chain A isoform 1
B: Beta-galactoside-specific lectin 1 chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,59820
Polymers55,8262
Non-polymers2,77218
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-76 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.859, 107.859, 311.386
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

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Beta-galactoside-specific lectin 1 chain ... , 2 types, 2 molecules AB

#1: Protein Beta-galactoside-specific lectin 1 chain A isoform 1 / Beta-galactoside-specific lectin I chain A isoform 1 / ML-I A / MLA / rRNA N-glycosidase


Mass: 27357.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: UniProt: P81446, rRNA N-glycosylase
#2: Protein Beta-galactoside-specific lectin 1 chain B / Beta-galactoside-specific lectin I chain B / ML-I B / MLB


Mass: 28467.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: UniProt: P81446

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Sugars , 3 types, 6 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-idopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpb1-4DIdopa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1212h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Idop]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 56 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 4.7 Å3/Da / Density % sol: 73.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 2.5 / Details: 0.2M Glycin, 30% AmSO4, 4% Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97621 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 16, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97621 Å / Relative weight: 1
ReflectionResolution: 2.28→40.77 Å / Num. obs: 48875 / % possible obs: 98 % / Redundancy: 15.8 % / Biso Wilson estimate: 68.39 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.013 / Rrim(I) all: 0.057 / Net I/σ(I): 37.7
Reflection shellResolution: 2.28→2.33 Å / Redundancy: 2 % / Rmerge(I) obs: 0.069 / Num. unique obs: 2047 / Rpim(I) all: 0.01676 / Rrim(I) all: 0.07199

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
autoPROCdata processing
XDSdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→40.77 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2312 2406 4.93 %
Rwork0.2095 --
obs0.2106 48810 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→40.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3949 0 149 44 4142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.007
X-RAY DIFFRACTIONf_dihedral_angle_d18.721612
X-RAY DIFFRACTIONf_chiral_restr0.061670
X-RAY DIFFRACTIONf_plane_restr0.008722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.330.33731310.29842725X-RAY DIFFRACTION100
2.33-2.380.30331320.27322726X-RAY DIFFRACTION100
2.38-2.430.3071490.2682711X-RAY DIFFRACTION100
2.43-2.490.29171410.25942752X-RAY DIFFRACTION100
2.49-2.560.36171520.25352728X-RAY DIFFRACTION100
2.56-2.640.33441450.27342736X-RAY DIFFRACTION100
2.64-2.720.32541400.28692731X-RAY DIFFRACTION100
2.72-2.820.27051370.26222750X-RAY DIFFRACTION100
2.82-2.930.29531470.25172750X-RAY DIFFRACTION100
2.93-3.060.28771400.25212758X-RAY DIFFRACTION100
3.06-3.230.25991380.25592776X-RAY DIFFRACTION100
3.23-3.430.2831330.24472792X-RAY DIFFRACTION100
3.43-3.690.23871270.22672467X-RAY DIFFRACTION88
3.69-4.060.23621100.20182206X-RAY DIFFRACTION78
4.06-4.650.1781580.16182829X-RAY DIFFRACTION100
4.65-5.860.19111340.17752910X-RAY DIFFRACTION100
5.86-40.770.2171920.2023057X-RAY DIFFRACTION100

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