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Yorodumi- PDB-1bvv: SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bvv | |||||||||
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Title | SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE | |||||||||
Components | ENDO-1,4-BETA-XYLANASEXylanase | |||||||||
Keywords | HYDROLASE / XYLANASE / GLYCOSIDASE / GLYCOSYL-ENZYME INTERMEDIATE / BOAT CONFORMATION / XYLAN DEGRADATION | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | |||||||||
Biological species | Bacillus circulans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | |||||||||
Authors | Sidhu, G. / Brayer, G.D. | |||||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase. Authors: Sidhu, G. / Withers, S.G. / Nguyen, N.T. / McIntosh, L.P. / Ziser, L. / Brayer, G.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bvv.cif.gz | 46.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bvv.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/1bvv ftp://data.pdbj.org/pub/pdb/validation_reports/bv/1bvv | HTTPS FTP |
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-Related 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: 20409.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 2-DEOXY-2-FLUORO-XYLOBIOSE COVALENTLY BONDED TO GLU 78 OE2 Source: (gene. exp.) Bacillus circulans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P09850, endo-1,4-beta-xylanase |
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-1,5-anhydro-2-deoxy-2-fluoro-D-xylitol Source method: isolated from a genetically manipulated source |
#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: 2.24 Å3/Da / Density % sol: 45.16 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→10 Å / Num. obs: 17727 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.6 |
Reflection | *PLUS % possible obs: 99 % / Num. measured all: 137937 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 4.9 |
-Processing
Software |
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Refinement | Resolution: 1.8→10 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |