[English] 日本語
Yorodumi- PDB-3ro8: Crystal structure of the catalytic domain of XynA1 from Paenibaci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ro8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the catalytic domain of XynA1 from Paenibacillus sp. JDR-2 | ||||||
Components | Endo-1,4-beta-xylanase | ||||||
Keywords | HYDROLASE / glycosyl hydrolase family 10 / GH10 / (beta/alpha)8 fold / Xylanase | ||||||
Function / homology | Function and homology information cell wall / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / extracellular region Similarity search - Function | ||||||
Biological species | Paenibacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Pozharski, E. / St John, F.J. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2012 Title: Novel structural features of xylanase A1 from Paenibacillus sp. JDR-2. Authors: St John, F.J. / Preston, J.F. / Pozharski, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ro8.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ro8.ent.gz | 943.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ro8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ro8_validation.pdf.gz | 499.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ro8_full_validation.pdf.gz | 541.1 KB | Display | |
Data in XML | 3ro8_validation.xml.gz | 124.6 KB | Display | |
Data in CIF | 3ro8_validation.cif.gz | 189.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ro/3ro8 ftp://data.pdbj.org/pub/pdb/validation_reports/ro/3ro8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
-Components
#1: Protein | Mass: 38401.809 Da / Num. of mol.: 8 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus sp. (bacteria) / Strain: JDR-2 / Gene: Pjdr2_0221 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C6CRV0, endo-1,4-beta-xylanase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.15 % |
---|---|
Crystal grow | Temperature: 294.5 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 200mM HEPES, 100 mM MgCl2, 18% PEG3350, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 294.5K |
-Data collection
Diffraction | Mean temperature: 105 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2008 Details: Rh coated flat mirror. side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→179.61 Å / Num. obs: 602662 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→42.61 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.94 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.38 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.34→42.61 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.34→1.377 Å / Total num. of bins used: 20
|