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Yorodumi- PDB-1isv: Crystal structure of xylanase from Streptomyces olivaceoviridis E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1isv | |||||||||
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Title | Crystal structure of xylanase from Streptomyces olivaceoviridis E-86 complexed with xylose | |||||||||
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 | 1isv.cif.gz | 195 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1isv.ent.gz | 152.5 KB | Display | PDB format |
PDBx/mmJSON format | 1isv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1isv_validation.pdf.gz | 458.7 KB | Display | wwPDB validaton report |
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Full document | 1isv_full_validation.pdf.gz | 472.5 KB | Display | |
Data in XML | 1isv_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 1isv_validation.cif.gz | 62 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/1isv ftp://data.pdbj.org/pub/pdb/validation_reports/is/1isv | HTTPS FTP |
-Related structure data
Related structure data | 1iswC 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: Sugar | ChemComp-XYP / #3: 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: 2.59 Å3/Da / Density % sol: 52.44 % | ||||||||||||||||||||||||||||||
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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 11, 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: 2.1→29.71 Å / Num. all: 404978 / Num. obs: 56890 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.77 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 5.75 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 7.7 / Num. unique all: 6558 / % possible all: 98.9 |
Reflection | *PLUS Num. measured all: 404978 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XYF Resolution: 2.1→29.71 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: 58.4226 Å2 / ksol: 0.414828 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→29.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009 / 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: 29.71 Å / Num. reflection obs: 65703 / σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor obs: 0.188 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24.4 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.07 Å / Rfactor Rfree: 0.275 / % reflection Rfree: 10.6 % / Rfactor Rwork: 0.284 / Num. reflection Rwork: 6500 / Rfactor obs: 0.284 |