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Yorodumi- PDB-3h2w: Structure of A. acidocaldarius cellulase CelA in complex with cel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h2w | |||||||||
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Title | Structure of A. acidocaldarius cellulase CelA in complex with cellobiose | |||||||||
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 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å | |||||||||
Authors | Morera, S. / 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 | 3h2w.cif.gz | 116.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h2w.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 3h2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h2w_validation.pdf.gz | 802 KB | Display | wwPDB validaton report |
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Full document | 3h2w_full_validation.pdf.gz | 806.7 KB | Display | |
Data in XML | 3h2w_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 3h2w_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/3h2w ftp://data.pdbj.org/pub/pdb/validation_reports/h2/3h2w | HTTPS FTP |
-Related structure data
Related structure data | 3gzkSC 3h3kC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59030.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicyclobacillus acidocaldarius (bacteria) Gene: celA / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star DE3 / References: UniProt: Q9AJS0, cellulase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-cellobiose |
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#3: Sugar | ChemComp-BGC / |
-Non-polymers , 4 types, 49 molecules
#4: Chemical | ChemComp-CA / | ||
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#5: Chemical | ChemComp-ZN / | ||
#6: Chemical | #7: 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 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.6M hexanediol, 100mM sodium acetate, pH5.0, 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: Oct 10, 2008 / Details: kirkpatrick baez |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→28 Å / Num. all: 16129 / Num. obs: 16129 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.66→2.82 Å / Redundancy: 6 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2504 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GZK Resolution: 2.66→25.92 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.866 / SU B: 12.875 / SU ML: 0.253 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.36 / 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: 24.857 Å2
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Refinement step | Cycle: LAST / Resolution: 2.66→25.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.66→2.729 Å / Total num. of bins used: 20
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