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Yorodumi- PDB-5i77: Crystal structure of a beta-1,4-endoglucanase from Aspergillus niger -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i77 | ||||||
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Title | Crystal structure of a beta-1,4-endoglucanase from Aspergillus niger | ||||||
Components | Endo-beta-1, 4-glucanase | ||||||
Keywords | HYDROLASE / substrate binding / endoglucanase | ||||||
Function / homology | Function and homology information cellulase / cellulase activity / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / extracellular region Similarity search - Function | ||||||
Biological species | Aspergillus niger (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Li, Y.J. / Liu, W.D. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2016 Title: Functional and structural analysis of Pichia pastoris-expressed Aspergillus niger 1,4-beta-endoglucanase Authors: Yan, J. / Liu, W. / Li, Y. / Lai, H.L. / Zheng, Y. / Huang, J.W. / Chen, C.C. / Chen, Y. / Jin, J. / Li, H. / 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 | 5i77.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i77.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 5i77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/5i77 ftp://data.pdbj.org/pub/pdb/validation_reports/i7/5i77 | HTTPS FTP |
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-Related structure data
Related structure data | 5i78C 5i79C 1gzjS 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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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 33735.945 Da / Num. of mol.: 1 / Fragment: UNP residues 31-331 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus niger (mold) / Gene: eg1 / Plasmid: pPICZaA / Production host: Escherichia coli (E. coli) / Strain (production host): P. Pastoris X33 / References: UniProt: A0A023UH08, UniProt: O74706*PLUS |
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#5: Sugar |
-Non-polymers , 4 types, 180 molecules
#2: Chemical | ChemComp-CA / | ||
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#3: Chemical | ChemComp-PGE / | ||
#4: Chemical | ChemComp-PEG / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.74 % / Mosaicity: 0.482 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG600, Ca(OAC)2, cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→25 Å / Num. obs: 28592 / % possible obs: 99.6 % / Redundancy: 8 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.019 / Rrim(I) all: 0.053 / Χ2: 1.006 / Net I/av σ(I): 43.729 / Net I/σ(I): 11.7 / Num. measured all: 230041 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GZJ Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.653 / SU ML: 0.11 / SU R Cruickshank DPI: 0.1346 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.139 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 84.55 Å2 / Biso mean: 31.769 Å2 / Biso min: 16.69 Å2
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Refinement step | Cycle: final / Resolution: 1.8→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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