+Open data
-Basic information
Entry | Database: PDB / ID: 1ia6 | ||||||
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Title | CRYSTAL STRUCTURE OF THE CELLULASE CEL9M OF C. CELLULOLYTICUM | ||||||
Components | CELLULASE CEL9M | ||||||
Keywords | HYDROLASE / Cellullase / Alpha Barrel | ||||||
Function / homology | Function and homology information cellulase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / polysaccharide catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Clostridium cellulolyticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 1ia6.cif.gz | 104 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ia6.ent.gz | 77.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ia6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ia6_validation.pdf.gz | 439.2 KB | Display | wwPDB validaton report |
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Full document | 1ia6_full_validation.pdf.gz | 440.3 KB | Display | |
Data in XML | 1ia6_validation.xml.gz | 19 KB | Display | |
Data in CIF | 1ia6_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/1ia6 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/1ia6 | HTTPS FTP |
-Related structure data
Related structure data | 1ia7C 1js4S 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: 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: UniProt: Q9EYQ2, cellulase |
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-Non-polymers , 5 types, 266 molecules
#2: Chemical | ChemComp-CA / |
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#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-NI / |
#5: Chemical | ChemComp-SO4 / |
#6: 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: 1.93 Å3/Da / Density % sol: 36.4 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulphate, calcium chloride, HEPES, 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: 290 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: Oct 14, 2000 / 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: 1.8→16 Å / Num. all: 170027 / Num. obs: 33837 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 6.6 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.9 / Num. unique all: 9028 / Rsym value: 23 / % possible all: 88.7 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 170027 / Rmerge(I) obs: 0.083 |
Reflection shell | *PLUS % possible obs: 88.7 % / Rmerge(I) obs: 0.295 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model with Cel9M sequence based on PDB ENTRY 1JS4. Resolution: 1.8→29.24 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1252803.33 / 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: The sequence in two flexible loops between L239 and N246 or A373 and D376 could not be fitted and is omitted. Mass spectrometric analysis has indicated that the sequence GTIVNPPVKK should ...Details: The sequence in two flexible loops between L239 and N246 or A373 and D376 could not be fitted and is omitted. 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: 49.21 Å2 / ksol: 0.377 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→29.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rfree: 0.189 / Rfactor Rwork: 0.158 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 1.86 Å / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.222 |