+Open data
-Basic information
Entry | Database: PDB / ID: 5d8w | ||||||
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Title | Structrue of a lucidum protein | ||||||
Components | Endoglucanase | ||||||
Keywords | HYDROLASE / GH5 family / Ganoderma lucidum / endoglucanase | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Ganoderma lucidum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.86 Å | ||||||
Authors | Guo, R. / Li, Q. / Shang, N. / Liu, G. / Ko, T.P. / Chen, C.C. / Liu, W. | ||||||
Citation | Journal: Enzyme.Microb.Technol. / Year: 2016 Title: Functional and structural analyses of a 1,4-beta-endoglucanase from Ganoderma lucidum. Authors: Liu, G. / Li, Q. / Shang, N. / Huang, J.W. / Ko, T.P. / Liu, W. / Zheng, Y. / Han, X. / Chen, Y. / Chen, C.C. / Jin, J. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d8w.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d8w.ent.gz | 104.8 KB | Display | PDB format |
PDBx/mmJSON format | 5d8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d8w_validation.pdf.gz | 433.3 KB | Display | wwPDB validaton report |
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Full document | 5d8w_full_validation.pdf.gz | 440.5 KB | Display | |
Data in XML | 5d8w_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 5d8w_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/5d8w ftp://data.pdbj.org/pub/pdb/validation_reports/d8/5d8w | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36738.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ganoderma lucidum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1A9TAJ1*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M Magnesium chloride hexahydrate, 0.1M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.86→25 Å / % possible obs: 93.2 % / Redundancy: 12.2 % / Net I/σ(I): 7.89 |
-Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.86→25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.903 / SU B: 16.354 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.395 / 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: 49.542 Å2
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Refinement step | Cycle: 1 / Resolution: 2.86→25 Å
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Refine LS restraints |
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