+Open data
-Basic information
Entry | Database: PDB / ID: 5gm3 | ||||||
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Title | Crystal structure of FI-CMCase from Aspergillus aculeatus F-50 | ||||||
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 / Resolution: 1.59 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 | 5gm3.cif.gz | 113.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gm3.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 5gm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gm3_validation.pdf.gz | 444.6 KB | Display | wwPDB validaton report |
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Full document | 5gm3_full_validation.pdf.gz | 446.5 KB | Display | |
Data in XML | 5gm3_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 5gm3_validation.cif.gz | 36.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/5gm3 ftp://data.pdbj.org/pub/pdb/validation_reports/gm/5gm3 | HTTPS FTP |
-Related structure data
Related structure data | 5gm4C 5gm5C 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 1 / Auth seq-ID: 4 - 220 / Label seq-ID: 2 - 218
NCS oper:
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-Components
#1: Protein | Mass: 23778.877 Da / Num. of mol.: 2 / Fragment: UNP residues 19-237 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus aculeatus (mold) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta2(DE3) / References: UniProt: P22669, cellulase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CAC / #4: 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: 2.76 Å3/Da / Density % sol: 55.42 % / Mosaicity: 0.425 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: sodium cacodylate, PEG 8000, 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: Sep 27, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.59→25 Å / Num. obs: 70687 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.075 / Net I/av σ(I): 27.317 / Net I/σ(I): 11.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KS4 Resolution: 1.59→25 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.367 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.075 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: 115.39 Å2 / Biso mean: 20.211 Å2 / Biso min: 6.6 Å2
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Refinement step | Cycle: final / Resolution: 1.59→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 1669 / Type: TIGHT THERMAL / Rms dev position: 2.75 Å / Weight position: 0.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.59→1.631 Å / Total num. of bins used: 20
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