+Open data
-Basic information
Entry | Database: PDB / ID: 6ifa | ||||||
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Title | Structure of beta-trefoil lectin from Entamoeba histolytica | ||||||
Components | lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / beta-trefoil / lectin / Entamoeba histolytica | ||||||
Function / homology | response to cation stress / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Ricin B, lectin domain / Ricin B-like lectins / carbohydrate binding / nucleus / ISOPROPYL ALCOHOL / Ricin-type beta-trefoil lectin domain containing protein Function and homology information | ||||||
Biological species | Entamoeba histolytica HM-1:IMSS (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Suguna, K. / Khan, F. | ||||||
Citation | Journal: Glycobiology / Year: 2020 Title: Crystal structures of a beta-trefoil lectin from Entamoeba histolytica in monomeric and a novel disulphide bond-mediated dimeric forms. Authors: Khan, F. / Kurre, D. / Suguna, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ifa.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ifa.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ifa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ifa_validation.pdf.gz | 463.2 KB | Display | wwPDB validaton report |
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Full document | 6ifa_full_validation.pdf.gz | 464.6 KB | Display | |
Data in XML | 6ifa_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 6ifa_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/6ifa ftp://data.pdbj.org/pub/pdb/validation_reports/if/6ifa | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | 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 / #3: Chemical | ChemComp-IPA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.52 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: 20% iso-propanol, 0.1M MES monohydrate, pH 6.0, 20% PEG monomethyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46 Å / SU ML: 0.2458 / Cross valid method: FREE R-VALUE / Phase error: 25.6638
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.51 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å
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