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Yorodumi- PDB-1v6w: Crystal Structure Of Xylanase From Streptomyces Olivaceoviridis E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v6w | |||||||||
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Title | Crystal Structure Of Xylanase From Streptomyces Olivaceoviridis E-86 Complexed With 2(2)-4-O-methyl-alpha-D-glucuronosyl-xylobiose | |||||||||
Components | ENDO-1,4-BETA-D-XYLANASEXylanase | |||||||||
Keywords | HYDROLASE / ALPHA-BETA BARREL / PROTEIN-SUGAR COMPLEX / CARBOHYDRATE BINDING MODULE | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Fujimoto, Z. / Kaneko, S. / Kuno, A. / Kobayashi, H. / Kusakabe, I. / Mizuno, H. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from Streptomyces olivaceoviridis E-86 Authors: Fujimoto, Z. / Kaneko, S. / Kuno, A. / Kobayashi, H. / Kusakabe, I. / Mizuno, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v6w.cif.gz | 199.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v6w.ent.gz | 155.8 KB | Display | PDB format |
PDBx/mmJSON format | 1v6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/1v6w ftp://data.pdbj.org/pub/pdb/validation_reports/v6/1v6w | HTTPS FTP |
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-Related structure data
Related structure data | 1v6uC 1v6vC 1v6xC 1iswS 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) Plasmid: pCR2.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SI98, endo-1,4-beta-xylanase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose | #4: Sugar | #5: 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: 2.74 Å3/Da / Density % sol: 55.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: AMMONIUM SULFATE, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→40.161 Å / Num. all: 68143 / Num. obs: 68143 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.082 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.2 / Num. unique all: 9443 / Rsym value: 0.228 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ISW Resolution: 2→29.52 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2315677.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.3754 Å2 / ksol: 0.366479 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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