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Yorodumi- PDB-1isw: Crystal structure of xylanase from Streptomyces olivaceoviridis E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1isw | |||||||||
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Title | Crystal structure of xylanase from Streptomyces olivaceoviridis E-86 complexed with xylobiose | |||||||||
Components | endo-1,4-beta-D-xylanase | |||||||||
Keywords | HYDROLASE / ALPHA-BETA BARREL / PROTEIN-SUGAR COMPLEX / CARBOHYDRATE BINDING DOMAIN | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / polysaccharide catabolic process Similarity search - Function | |||||||||
Biological species | Streptomyces olivaceoviridis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Fujimoto, Z. / Kuno, A. / Kaneko, S. / Kobayashi, H. / Kusakabe, I. / Mizuno, H. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structures of the sugar complexes of Streptomyces olivaceoviridis E-86 xylanase: sugar binding structure of the family 13 carbohydrate binding module. Authors: Fujimoto, Z. / Kuno, A. / Kaneko, S. / Kobayashi, H. / Kusakabe, I. / Mizuno, H. #1: Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structure of Streptomyces olivaceoviridis E-86 beta-xylanase containing xylan-binding domain Authors: Fujimoto, Z. / Kuno, A. / Kaneko, S. / Yoshida, S. / Kobayashi, H. / Kusakabe, I. / Mizuno, H. #2: Journal: J.BIOCHEM.(TOKYO) / Year: 1997 Title: Crystallization and preliminary X-ray crystallographic study of Streptomyces olivaceoviridis E-86 beta-xylanase Authors: Fujimoto, Z. / Mizuno, H. / Kuno, A. / Yoshida, S. / Kobayashi, H. / Kusakabe, I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1isw.cif.gz | 195.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1isw.ent.gz | 153.4 KB | Display | PDB format |
PDBx/mmJSON format | 1isw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1isw_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1isw_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 1isw_validation.xml.gz | 41 KB | Display | |
Data in CIF | 1isw_validation.cif.gz | 61 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/1isw ftp://data.pdbj.org/pub/pdb/validation_reports/is/1isw | HTTPS FTP |
-Related structure data
Related structure data | 1isvC 1isxC 1isyC 1iszC 1it0C 1xyfS 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
#1: Protein | Mass: 46791.223 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces olivaceoviridis (bacteria) Strain: E-86 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SI98, endo-1,4-beta-xylanase #2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose #3: Sugar | ChemComp-XYP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.77 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: ammonium sulfate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
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 RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 12, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→46 Å / Num. all: 359683 / Num. obs: 66842 / % possible obs: 86.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.22 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 6.4 / Num. unique all: 6586 / % possible all: 77.7 |
Reflection | *PLUS Num. measured all: 359683 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XYF Resolution: 2.1→29.74 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.7471 Å2 / ksol: 0.39314 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→29.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10.2 % / Rfactor obs: 0.196 / Rfactor Rfree: 0.244 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.18 Å / % reflection Rfree: 11.1 % / Rfactor Rwork: 0.244 / Num. reflection Rwork: 4447 / Rfactor obs: 0.244 |