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- PDB-6ifa: Structure of beta-trefoil lectin from Entamoeba histolytica -

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Basic information

Entry
Database: PDB / ID: 6ifa
TitleStructure of beta-trefoil lectin from Entamoeba histolytica
Componentslectin
KeywordsSUGAR BINDING PROTEIN / beta-trefoil / lectin / Entamoeba histolytica
Function / homologyRicin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Ricin B, lectin domain / Ricin B-like lectins / carbohydrate binding / ISOPROPYL ALCOHOL / Ricin-type beta-trefoil lectin domain containing protein
Function and homology information
Biological speciesEntamoeba histolytica HM-1:IMSS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSuguna, K. / Khan, F.
CitationJournal: Glycobiology / Year: 2020
Title: Crystal structures of a beta-trefoil lectin from Entamoeba histolytica in monomeric and a novel disulfide bond-mediated dimeric forms.
Authors: Khan, F. / Kurre, D. / Suguna, K.
History
DepositionSep 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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: lectin
B: lectin
C: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,03417
Polymers44,0323
Non-polymers1,00114
Water3,081171
1
A: lectin
B: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,08412
Polymers29,3552
Non-polymers72910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-7 kcal/mol
Surface area11260 Å2
MethodPISA
2
C: lectin
hetero molecules

C: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,90010
Polymers29,3552
Non-polymers5458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_554-y+1/2,-x+1/2,-z-1/21
Buried area1350 Å2
ΔGint-9 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.732, 101.732, 183.996
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein lectin


Mass: 14677.430 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS (eukaryote)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: N9TFI9*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 20% iso-propanol, 0.1M MES monohydrate, pH 6.0, 20% PEG monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.9→46 Å / Num. obs: 38368 / % possible obs: 99.9 % / Redundancy: 13.23 % / Biso Wilson estimate: 27.15 Å2 / CC1/2: 0.99 / Net I/σ(I): 13.88
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 12.43 % / Mean I/σ(I) obs: 1.75 / Num. unique obs: 6102 / CC1/2: 0.84 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
REFMAC5refinement
XDS2018-04-27data reduction
XDS2018-04-27data scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46 Å / SU ML: 0.2458 / Cross valid method: FREE R-VALUE / Phase error: 25.6638
RfactorNum. reflection% reflection
Rfree0.2364 1917 5 %
Rwork0.194 --
obs0.1962 38304 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.51 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3027 0 66 171 3264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673194
X-RAY DIFFRACTIONf_angle_d0.80134332
X-RAY DIFFRACTIONf_chiral_restr0.0608471
X-RAY DIFFRACTIONf_plane_restr0.0053564
X-RAY DIFFRACTIONf_dihedral_angle_d8.54652596
LS refinement shellResolution: 1.9→1.95 Å
RfactorNum. reflection% reflection
Rfree0.3459 135 -
Rwork0.2807 2558 -
obs--99.8 %

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