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- PDB-5zbt: Structure of legume lectin-like domain from Entamoeba histolytica -

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Basic information

Entry
Database: PDB / ID: 5zbt
TitleStructure of legume lectin-like domain from Entamoeba histolytica
ComponentsLectin-like protein
KeywordsUNKNOWN FUNCTION / ERGIC-like
Function / homologyLegume-like lectin / : / Legume-like lectin family / L-type lectin-like (leguminous) domain profile. / carbohydrate binding / Concanavalin A-like lectin/glucanase domain superfamily / membrane / Vesicular mannose-binding lectin, putative
Function and homology information
Biological speciesEntamoeba histolytica HM-1:IMSS-A (eukaryote)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.4 Å
AuthorsKhan, F. / Suguna, K.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: Crystal structure of the legume lectin-like domain of an ERGIC-53-like protein from Entamoeba histolytica
Authors: Khan, F. / Suguna, K.
History
DepositionFeb 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Lectin-like protein


Theoretical massNumber of molelcules
Total (without water)28,3571
Polymers28,3571
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9960 Å2
Unit cell
Length a, b, c (Å)56.051, 57.174, 72.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lectin-like protein


Mass: 28356.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS-A (eukaryote)
Gene: EHI7A_000050 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: N9T8S1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.05 Å3/Da / Density % sol: 40.1 %
Crystal growTemperature: 289 K / Method: microbatch / pH: 6.5
Details: 0.1M Bis-Tris, pH 6.5, 28%(w/v) PEG monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 2.28977 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.28977 Å / Relative weight: 1
ReflectionResolution: 2.3→44.93 Å / Num. obs: 10084 / % possible obs: 93 % / Redundancy: 13.9 % / Net I/σ(I): 38.47
Reflection shellResolution: 2.3→2.38 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→26.594 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 469 5 %RANDOM
Rwork0.175 ---
obs0.1769 9374 98.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→26.594 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1658 0 0 106 1764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081692
X-RAY DIFFRACTIONf_angle_d0.9592290
X-RAY DIFFRACTIONf_dihedral_angle_d6.741017
X-RAY DIFFRACTIONf_chiral_restr0.061256
X-RAY DIFFRACTIONf_plane_restr0.005293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3997-2.74660.24711470.18262784X-RAY DIFFRACTION94
2.7466-3.45920.23981580.1873002X-RAY DIFFRACTION100
3.4592-26.59540.18221640.16473119X-RAY DIFFRACTION100

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