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Yorodumi- PDB-2z48: Crystal Structure of Hemolytic Lectin CEL-III Complexed with GalNac -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z48 | ||||||||||||
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Title | Crystal Structure of Hemolytic Lectin CEL-III Complexed with GalNac | ||||||||||||
Components | Hemolytic lectin CEL-III | ||||||||||||
Keywords | TOXIN / Lectin / CEL-III / Hemolysis / Hemagglutination / Pore-forming / Calcium / Magnesium / GalNac | ||||||||||||
Function / homology | Function and homology information positive regulation of erythrocyte aggregation / melibiose binding / cell killing / N-acetylgalactosamine binding / polypeptide N-acetylgalactosaminyltransferase activity / fucose binding / disruption of plasma membrane integrity in another organism / lactose binding / hemolysis in another organism / galactose binding ...positive regulation of erythrocyte aggregation / melibiose binding / cell killing / N-acetylgalactosamine binding / polypeptide N-acetylgalactosaminyltransferase activity / fucose binding / disruption of plasma membrane integrity in another organism / lactose binding / hemolysis in another organism / galactose binding / protein O-linked glycosylation / protein homooligomerization / antibacterial humoral response / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / calcium ion binding / Golgi apparatus / magnesium ion binding / extracellular space Similarity search - Function | ||||||||||||
Biological species | Cucumaria echinata (invertebrata) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||||||||
Authors | Hatakeyama, T. / Unno, H. / Eto, S. / Hidemura, H. / Uchida, T. / Kouzuma, Y. | ||||||||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: C-type lectin-like carbohydrate-recognition of the hemolytic lectin CEL-III containing ricin-type beta-trefoil folds Authors: Hatakeyama, T. / Unno, H. / Kouzuma, Y. / Uchida, T. / Eto, S. / Hidemura, H. / Kato, N. / Yonekura, M. / Kusunoki, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z48.cif.gz | 203.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z48.ent.gz | 158.6 KB | Display | PDB format |
PDBx/mmJSON format | 2z48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z4/2z48 ftp://data.pdbj.org/pub/pdb/validation_reports/z4/2z48 | HTTPS FTP |
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-Related structure data
Related structure data | 2z49C 1vclS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 1 / Auth seq-ID: 2 - 432 / Label seq-ID: 2 - 432
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 47452.164 Da / Num. of mol.: 2 / Fragment: residues in database 11-442 / Mutation: Q11PCA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cucumaria echinata (invertebrata) / Production host: Escherichia coli / References: UniProt: Q868M7 |
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-Sugars , 2 types, 12 molecules
#2: Sugar | ChemComp-A2G / #3: Sugar | ChemComp-NGA / |
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-Non-polymers , 3 types, 852 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THERE ARE 13 DIFFERENCES BETWEEN THE DEPOSITORS DATA AND THE GENETIC SEQUENCE. THERE IS NO QUESTION ...THERE ARE 13 DIFFERENCE |
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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: 2.3 Å3/Da / Density % sol: 46.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10mM GalNac, 12% PEG 8000, 100mM Bis-Tris/NaOH, 200mM magnesium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: BRUKER DIP-6040B / Detector: IMAGE PLATE / Date: Oct 2, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→64.96 Å / Num. obs: 89844 / % possible obs: 96.4 % / Redundancy: 2 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 2 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 3.5 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VCL Resolution: 1.7→64.96 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.14 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.532 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→64.96 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3306 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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