+Open data
-Basic information
Entry | Database: PDB / ID: 3gzk | ||||||
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Title | Structure of A. Acidocaldarius Cellulase CelA | ||||||
Components | Cellulase | ||||||
Keywords | HYDROLASE / fold from GH9 from CAZY database / Glycosidase | ||||||
Function / homology | Function and homology information cellulase / cellulase activity / cellulose catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Morera, S. / Eckert, K. / Vigouroux, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Crystal structures of A. acidocaldarius endoglucanase Cel9A in complex with cello-oligosaccharides: strong -1 and -2 subsites mimic cellobiohydrolase activity Authors: Eckert, K. / Vigouroux, A. / Lo Leggio, L. / Morera, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gzk.cif.gz | 122.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gzk.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 3gzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/3gzk ftp://data.pdbj.org/pub/pdb/validation_reports/gz/3gzk | HTTPS FTP |
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-Related structure data
Related structure data | 3h2wC 3h3kC 1clcS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 59030.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria) Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star DE3 / References: UniProt: Q9AJS0, cellulase | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | #5: 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: 2.28 Å3/Da / Density % sol: 46.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50% MPD, 100mM Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2008 / Details: Kirkpatrick Baez |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 50946 / Num. obs: 50946 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.24 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 6 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2.3 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CLC Resolution: 1.8→19.73 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.603 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.118 / 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: 18.137 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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