+Open data
-Basic information
Entry | Database: PDB / ID: 5d61 | |||||||||
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Title | MOA-Z-VAD-fmk complex, direct orientation | |||||||||
Components |
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Keywords | HYDROLASE / papain-like / inhibitor / protease / fungal | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Marasmius oreades (fairy-ring mushroom) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Cordara, G. / van Eerde, A. / Grahn, E.M. / Goldstein, I.J. / Krengel, U. | |||||||||
Citation | Journal: Plos One / Year: 2016 Title: An Unusual Member of the Papain Superfamily: Mapping the Catalytic Cleft of the Marasmius oreades agglutinin (MOA) with a Caspase Inhibitor. Authors: Cordara, G. / van Eerde, A. / Grahn, E.M. / Winter, H.C. / Goldstein, I.J. / Krengel, U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d61.cif.gz | 85.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d61.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 5d61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d61_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5d61_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5d61_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 5d61_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/5d61 ftp://data.pdbj.org/pub/pdb/validation_reports/d6/5d61 | HTTPS FTP |
-Related structure data
Related structure data | 5d62C 5d63C 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 / Protein/peptide , 2 types, 2 molecules AL
#1: Protein | Mass: 32328.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marasmius oreades (fairy-ring mushroom) Plasmid: pT7-LO / Details (production host): IPTG-inducible / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8X123 |
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#2: Protein/peptide | |
-Sugars , 2 types, 3 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 | Source method: isolated from a genetically manipulated source |
-Non-polymers , 6 types, 270 molecules
#5: Chemical | #6: Chemical | ChemComp-CL / | #7: Chemical | #8: Chemical | ChemComp-DMS / | #9: Chemical | ChemComp-NA / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.62 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M imidazole pH 8.0, 12% PEG 8000, 0.2 M calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 31, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→46.31 Å / Num. all: 56827 / Num. obs: 56827 / % possible obs: 99.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.7 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EF2 Resolution: 1.6→46.3 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.289 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.068 / 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: 19.32 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→46.3 Å
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Refine LS restraints |
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