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Yorodumi- PDB-5gm5: Crystal structure of FI-CMCase from Aspergillus aculeatus F-50 in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gm5 | |||||||||
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Title | Crystal structure of FI-CMCase from Aspergillus aculeatus F-50 in complex with cellobiose | |||||||||
Components | Endoglucanase-1 | |||||||||
Keywords | HYDROLASE/INHIBITOR / substrate binding / HYDROLASE-INHIBITOR complex | |||||||||
Function / homology | Function and homology information cellulase / cellulase activity / cellulose catabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Aspergillus aculeatus (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å | |||||||||
Authors | Huang, J.W. / Liu, W.D. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T. | |||||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2016 Title: Crystal structure and genetic modifications of FI-CMCase from Aspergillus aculeatus F-50 Authors: Huang, J.W. / Liu, W. / Lai, H.L. / Cheng, Y.S. / Zheng, Y. / Li, Q. / Sun, H. / Kuo, C.J. / Guo, R.T. / Chen, C.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gm5.cif.gz | 336.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gm5.ent.gz | 270.9 KB | Display | PDB format |
PDBx/mmJSON format | 5gm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gm5_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 5gm5_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 5gm5_validation.xml.gz | 71.3 KB | Display | |
Data in CIF | 5gm5_validation.cif.gz | 105.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/5gm5 ftp://data.pdbj.org/pub/pdb/validation_reports/gm/5gm5 | HTTPS FTP |
-Related structure data
Related structure data | 5gm3C 5gm4C 1ks4S 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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7 |
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Unit cell |
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-Components
#1: Protein | Mass: 23848.977 Da / Num. of mol.: 7 / Fragment: UNP residues 18-237 / Mutation: E202A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus aculeatus (mold) / Plasmid: pPICZaA / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: P22669, cellulase #2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-EPE / | #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: 2.39 Å3/Da / Density % sol: 48.45 % / Mosaicity: 0.66 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: lithium sulfate, HEPES, zinc acetate, |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.73→25 Å / Num. obs: 163715 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.041 / Rrim(I) all: 0.076 / Χ2: 0.937 / Net I/av σ(I): 17.737 / Net I/σ(I): 9.3 / Num. measured all: 558314 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1KS4 Resolution: 1.73→25 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.164 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.095 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: 95.05 Å2 / Biso mean: 20.371 Å2 / Biso min: 9.26 Å2
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Refinement step | Cycle: final / Resolution: 1.73→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.775 Å / Total num. of bins used: 20
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