[English] 日本語
Yorodumi- PDB-1v6u: Crystal Structure Of Xylanase From Streptomyces Olivaceoviridis E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v6u | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure Of Xylanase From Streptomyces Olivaceoviridis E-86 Complexed With 2(2)-alpha-L-arabinofuranosyl-xylobiose | |||||||||
Components | endo-1,4-beta-D-xylanase | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1v6u.cif.gz | 192.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1v6u.ent.gz | 151.4 KB | Display | PDB format |
PDBx/mmJSON format | 1v6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v6u_validation.pdf.gz | 683.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1v6u_full_validation.pdf.gz | 694.7 KB | Display | |
Data in XML | 1v6u_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 1v6u_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/1v6u ftp://data.pdbj.org/pub/pdb/validation_reports/v6/1v6u | HTTPS FTP |
-Related structure data
Related structure data | 1v6vC 1v6wC 1v6xC 1iswS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Non-polymers , 2 types, 631 molecules AB
#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 #6: Water | ChemComp-HOH / | |
---|
-Sugars , 4 types, 9 molecules
#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | #5: Sugar | ChemComp-XYS / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.86 % |
---|---|
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 |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 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→27.05 Å / Num. all: 57787 / Num. obs: 57787 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.06 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 1.99 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 2.1 / Num. unique all: 10362 / % possible all: 98.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ISW Resolution: 2.1→27.05 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 415170.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 68.0249 Å2 / ksol: 0.403183 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.2 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→27.05 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|