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Yorodumi- PDB-6tsn: Marasmius oreades agglutinin (MOA), papain back.swap W208Q-Q276W ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tsn | ||||||
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Title | Marasmius oreades agglutinin (MOA), papain back.swap W208Q-Q276W variant | ||||||
Components | Agglutinin | ||||||
Keywords | SUGAR BINDING PROTEIN / fungal chimerolectin / papain-like cysteine protease / protease-substrate complex / calcium-binding protein / manganese-binding protein / toxin | ||||||
Function / homology | Agglutinin, C-terminal / Agglutinin C-terminal / Ricin-type beta-trefoil lectin domain-like / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Papain-like cysteine peptidase superfamily / metal ion binding / Agglutinin Function and homology information | ||||||
Biological species | Marasmius oreades (fairy-ring mushroom) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Cordara, G. / Manna, D. / Krengel, U. | ||||||
Citation | Journal: Curr Res Struct Biol / Year: 2020 Title: Crystal structure of MOA in complex with a peptide fragment: A protease caught in flagranti . Authors: Manna, D. / Cordara, G. / Krengel, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tsn.cif.gz | 86.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tsn.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6tsn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/6tsn ftp://data.pdbj.org/pub/pdb/validation_reports/ts/6tsn | HTTPS FTP |
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-Related structure data
Related structure data | 6tslC 6tsmC 6tsoC 6tsqC 6tsrC 6yh0C 3ef2S 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 32419.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marasmius oreades (fairy-ring mushroom) Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q8X123 |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 5 types, 202 molecules
#4: Chemical | ChemComp-EDO / | ||||
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#5: Chemical | ChemComp-DMS / | ||||
#6: Chemical | #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 3.3 Å3/Da / Density % sol: 63.2 % / Description: rod-shaped crystals |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M cacodylate/HCl pH 6.5, 14% PEG 8000, 0.2 M calcium acetate, 10% DMSO, 5 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 16, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→46.6 Å / Num. obs: 104686 / % possible obs: 94.8 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.051 / Rrim(I) all: 0.145 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.749 / Num. unique obs: 2154 / CC1/2: 0.265 / Rpim(I) all: 1.572 / Rrim(I) all: 2.359 / % possible all: 77.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EF2 Resolution: 1.6→46.6 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.572 / SU ML: 0.051 / Cross valid method: FREE R-VALUE / ESU R: 0.077 / ESU R Free: 0.078 Details: Hydrogens have been added in their 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.138 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→46.6 Å
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Refine LS restraints |
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LS refinement shell |
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