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Yorodumi- PDB-5m6g: Crystal structure Glucan 1,4-beta-glucosidase from Saccharopolysp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m6g | ||||||
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Title | Crystal structure Glucan 1,4-beta-glucosidase from Saccharopolyspora erythraea | ||||||
Components | Beta-glucosidase | ||||||
Keywords | HYDROLASE / 2-DOMAIN FOLD | ||||||
Function / homology | Function and homology information glucan 1,4-beta-glucosidase / glucan 1,4-beta-glucosidase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Saccharopolyspora erythraea D (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.829 Å | ||||||
Authors | Gabdulkhakov, A. / Tishchenko, S. / Lisov, A. / Leontievsky, A. | ||||||
Citation | Journal: To Be Published Title: Crystal structure Glucan 1,4-beta-glucosidase from Saccharopolyspora erythraea Authors: Gabdulkhakov, A. / Tishchenko, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m6g.cif.gz | 131.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m6g.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 5m6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m6g_validation.pdf.gz | 462.1 KB | Display | wwPDB validaton report |
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Full document | 5m6g_full_validation.pdf.gz | 464.2 KB | Display | |
Data in XML | 5m6g_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 5m6g_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/5m6g ftp://data.pdbj.org/pub/pdb/validation_reports/m6/5m6g | HTTPS FTP |
-Related structure data
Related structure data | 1ieqS 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 / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 65379.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharopolyspora erythraea D (bacteria) Strain: ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338 Gene: celD, SACE_6502, A8924_6851 / Production host: Komagataella pastoris GS115 (fungus) / References: UniProt: A4FNP6, glucan 1,4-beta-glucosidase |
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#5: Sugar | ChemComp-SOR / |
-Non-polymers , 4 types, 288 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-PGE / | #6: 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: 2.12 Å3/Da / Density % sol: 41.98 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% PEG 20K, 100mM MES Sodium Salt, 80 mM Mangan II Chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033121 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033121 Å / Relative weight: 1 |
Reflection | Resolution: 1.829→50 Å / Num. obs: 47457 / % possible obs: 95.1 % / Redundancy: 3.35 % / Net I/σ(I): 11.27 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ieq Resolution: 1.829→45.511 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.829→45.511 Å
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Refine LS restraints |
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LS refinement shell |
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