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Yorodumi- PDB-6tsm: Marasmius oreades agglutinin (MOA) in complex with the truncated ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tsm | ||||||
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Title | Marasmius oreades agglutinin (MOA) in complex with the truncated PVVRAHS synthetic substrate | ||||||
Components |
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Keywords | SUGAR BINDING PROTEIN / fungal chimerolectin / papain-like cysteine protease / protease-substrate complex / calcium-binding protein / manganese-binding protein | ||||||
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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 | 6tsm.cif.gz | 87.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tsm.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6tsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/6tsm ftp://data.pdbj.org/pub/pdb/validation_reports/ts/6tsm | HTTPS FTP |
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-Related structure data
Related structure data | 6tslC 6tsnC 6tsoC 6tsqC 6tsrC 6yh0C 3ef2S C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein / Protein/peptide , 2 types, 2 molecules AAABBB
#1: Protein | Mass: 32229.578 Da / Num. of mol.: 1 / Mutation: C215A, H257A 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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#2: Protein/peptide | Mass: 470.585 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: synthetic proteolysis substrate / Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
-Sugars , 2 types, 2 molecules
#3: Polysaccharide | alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 256 molecules
#5: Chemical | #6: Chemical | ChemComp-EDO / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-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 crystal |
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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, 20% PEG 8000, 0.2 M sodium acetate, 10 mM CaCl2, 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: ID29 / Wavelength: 0.97239 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97239 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→46.8 Å / Num. obs: 87357 / % possible obs: 99.8 % / Redundancy: 19.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.035 / Rrim(I) all: 0.152 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 17.8 % / Rmerge(I) obs: 5.335 / Mean I/σ(I) obs: 0.362 / Num. unique obs: 4152 / CC1/2: 0.362 / Rpim(I) all: 1.266 / Rrim(I) all: 5.489 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EF2 Resolution: 1.4→46.8 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.296 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.051 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: 20.883 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→46.8 Å
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Refine LS restraints |
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LS refinement shell |
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