[English] 日本語
Yorodumi- PDB-1v6v: Crystal Structure Of Xylanase From Streptomyces Olivaceoviridis E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v6v | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure Of Xylanase From Streptomyces Olivaceoviridis E-86 Complexed With 3(2)-alpha-L-arabinofuranosyl-xylotriose | |||||||||
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 / SYNCHROTRON / 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 | 1v6v.cif.gz | 200.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1v6v.ent.gz | 158.4 KB | Display | PDB format |
PDBx/mmJSON format | 1v6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v6v_validation.pdf.gz | 733.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1v6v_full_validation.pdf.gz | 743.6 KB | Display | |
Data in XML | 1v6v_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 1v6v_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/1v6v ftp://data.pdbj.org/pub/pdb/validation_reports/v6/1v6v | HTTPS FTP |
-Related structure data
Related structure data | 1v6uC 1v6wC 1v6xC 1isxS 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, 942 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, 8 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | #4: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose | #5: Sugar | ChemComp-XYP / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.17 % |
---|---|
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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30.015 Å / Num. all: 80990 / Num. obs: 80990 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.058 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 3 / Num. unique all: 11809 / Rsym value: 0.236 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ISX Resolution: 2.1→29.97 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2378187.82 / 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: 61.1435 Å2 / ksol: 0.415883 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→29.97 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|