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Yorodumi- PDB-1j01: Crystal Structure Of The Xylanase Cex With Xylobiose-Derived Inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j01 | |||||||||
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Title | Crystal Structure Of The Xylanase Cex With Xylobiose-Derived Inhibitor Isofagomine lactam | |||||||||
Components | beta-1,4-xylanase | |||||||||
Keywords | HYDROLASE / CEX / XYLANASE / DEOXYNOJIRIMYCIN INHIBITOR / CELLULOSE DEGRADATION | |||||||||
Function / homology | Function and homology information cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / polysaccharide binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / cellulose catabolic process Similarity search - Function | |||||||||
Biological species | Cellulomonas fimi (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Williams, S.J. / Notenboom, V. / Wicki, J. / Rose, D.R. / Withers, S.G. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2000 Title: A New, Simple, High-Affinity Glycosidase Inhibitor: Analysis of Binding through X-ray Crystallography, Mutagenesis, and Kinetic Analysis Authors: Williams, S.J. / Notenboom, V. / Wicki, J. / Rose, D.R. / Withers, S.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j01.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j01.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 1j01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/1j01 ftp://data.pdbj.org/pub/pdb/validation_reports/j0/1j01 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 34051.941 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellulomonas fimi (bacteria) / Gene: Cex / Plasmid: pUC12 / Production host: Escherichia coli (E. coli) References: UniProt: P07986, cellulose 1,4-beta-cellobiosidase (non-reducing end) |
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#2: Sugar | ChemComp-XIL / ( |
#3: 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: 2.23 Å3/Da / Density % sol: 44.89 % | |||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||
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: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 2000 |
Radiation | Monochromator: Osmic focussing optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 21434 / Num. obs: 20862 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2→2.1 Å / % possible all: 85 |
Reflection | *PLUS Num. obs: 21259 / % possible obs: 99 % / Num. measured all: 258208 / Rmerge(I) obs: 0.057 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→500 Å
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Refinement | *PLUS Lowest resolution: 500 Å / Rfactor Rfree: 0.25 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |