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Yorodumi- PDB-5l9c: Crystal structure of an endoglucanase from Penicillium verruculos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l9c | |||||||||
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Title | Crystal structure of an endoglucanase from Penicillium verruculosum in complex with cellobiose | |||||||||
Components | endoglucanase | |||||||||
Keywords | HYDROLASE / endohydrolysis / cellulose | |||||||||
Function / homology | Function and homology information cellulase / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | |||||||||
Biological species | Talaromyces verruculosus (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Nemashkalov, V. / Vakhrusheva, A. / Tishchenko, S. / Gabdulkhakov, A. / Kravchenko, O. / Gusakov, A. / Sinisyn, A. | |||||||||
Funding support | Russian Federation, 1items
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Citation | Journal: to be published Title: Crystal structure of an endoglucanase from Penicillium verruculosum in complex with cellobiose Authors: Nemashkalov, V. / Vakhrusheva, A. / Tishchenko, S. / Gabdulkhakov, A. / Kravchenko, O. / Gusakov, A. / Sinisyn, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l9c.cif.gz | 282.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l9c.ent.gz | 225.7 KB | Display | PDB format |
PDBx/mmJSON format | 5l9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l9c_validation.pdf.gz | 3.6 MB | Display | wwPDB validaton report |
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Full document | 5l9c_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 5l9c_validation.xml.gz | 59 KB | Display | |
Data in CIF | 5l9c_validation.cif.gz | 91.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/5l9c ftp://data.pdbj.org/pub/pdb/validation_reports/l9/5l9c | HTTPS FTP |
-Related structure data
Related structure data | 5i6sS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 34645.805 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Talaromyces verruculosus (fungus) / Production host: Talaromyces verruculosus (fungus) / References: UniProt: A0A1U7Q1U3*PLUS #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose #4: Sugar | #5: 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: 2.41 Å3/Da / Density % sol: 48.88 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop Details: 20% polyethylene glycole 6000, 50 mM bis-tris propane pH 7.0, 7% 2 methyl-2,4,-pentanediol, 5% 2 methyl-2 propanal, 6% PEG 5000, cellobiose |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→48.4 Å / Num. obs: 107169 / % possible obs: 90 % / Redundancy: 1.83 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.78→1.83 Å / Rmerge(I) obs: 0.498 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I6S Resolution: 1.85→48.398 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→48.398 Å
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Refine LS restraints |
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LS refinement shell |
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