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Yorodumi- PDB-1ia7: CRYSTAL STRUCTURE OF THE CELLULASE CEL9M OF C. CELLULOLYTICIUM IN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ia7 | |||||||||
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Title | CRYSTAL STRUCTURE OF THE CELLULASE CEL9M OF C. CELLULOLYTICIUM IN COMPLEX WITH CELLOBIOSE | |||||||||
Components | CELLULASE CEL9M | |||||||||
Keywords | HYDROLASE / Cellulase / alpha barrel | |||||||||
Function / homology | Function and homology information Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulase activity / polysaccharide catabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Clostridium cellulolyticum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Parsiegla, G. / Belaich, A. / Belaich, J.P. / Haser, R. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Crystal structure of the cellulase Cel9M enlightens structure/function relationships of the variable catalytic modules in glycoside hydrolases. Authors: Parsiegla, G. / Belaich, A. / Belaich, J.P. / Haser, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ia7.cif.gz | 108.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ia7.ent.gz | 80 KB | Display | PDB format |
PDBx/mmJSON format | 1ia7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ia7_validation.pdf.gz | 770.7 KB | Display | wwPDB validaton report |
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Full document | 1ia7_full_validation.pdf.gz | 774.1 KB | Display | |
Data in XML | 1ia7_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 1ia7_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/1ia7 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/1ia7 | HTTPS FTP |
-Related structure data
Related structure data | 1ia6SC 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 / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 48697.875 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium cellulolyticum (bacteria) / Production host: Escherichia coli (E. coli) References: GenBank: 12007368, UniProt: Q9EYQ2*PLUS, cellulase |
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose |
-Non-polymers , 6 types, 333 molecules
#3: Chemical | ChemComp-CA / | ||
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#4: Chemical | ChemComp-ZN / | ||
#5: Chemical | ChemComp-NI / | ||
#6: Chemical | ChemComp-SO4 / | ||
#7: Chemical | #8: 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: 1.9 Å3/Da / Density % sol: 35.36 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulfate, calcium chloride, Hepes, Ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FU581 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 23, 2001 / Details: Osmic confocal mirrors |
Radiation | Monochromator: confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→16 Å / Num. all: 110767 / Num. obs: 24339 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.095 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2244 / Rsym value: 0.315 / % possible all: 94.3 |
Reflection | *PLUS Lowest resolution: 16 Å / Num. measured all: 110767 / Rmerge(I) obs: 0.12 |
Reflection shell | *PLUS % possible obs: 94.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IA6 Resolution: 2→16.23 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1284072.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Mass spectrometric analysis has indicated that the sequence GTIVNPPVKK should additionally be present at the C-terminus in the crystal, but it could not be traced in the electron density.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.32 Å2 / ksol: 0.434 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→16.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 16 Å / Rfactor Rfree: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.07 Å |