+Open data
-Basic information
Entry | Database: PDB / ID: 2dcy | |||||||||
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Title | Crystal structure of Bacillus subtilis family-11 xylanase | |||||||||
Components | Endo-1,4-beta-xylanase A | |||||||||
Keywords | HYDROLASE / ALL BETA | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Kondo, H. / Miyazaki, K. / Takenouchi, M. / Noro, N. / Suzuki, M. / Tsuda, S. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Thermal Stabilization of Bacillus subtilis Family-11 Xylanase by Directed Evolution Authors: Miyazaki, K. / Takenouchi, M. / Kondo, H. / Noro, N. / Suzuki, M. / Tsuda, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dcy.cif.gz | 192.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dcy.ent.gz | 153.5 KB | Display | PDB format |
PDBx/mmJSON format | 2dcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dcy_validation.pdf.gz | 497.6 KB | Display | wwPDB validaton report |
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Full document | 2dcy_full_validation.pdf.gz | 511 KB | Display | |
Data in XML | 2dcy_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | 2dcy_validation.cif.gz | 50.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/2dcy ftp://data.pdbj.org/pub/pdb/validation_reports/dc/2dcy | HTTPS FTP |
-Related structure data
Related structure data | 2dczC 1xnbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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5 |
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Unit cell |
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-Components
#1: Protein | Mass: 20394.979 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: xynA / Plasmid: pTD-tac / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P18429, endo-1,4-beta-xylanase #2: Chemical | #3: Chemical | ChemComp-TLA / #4: Chemical | ChemComp-TAR / | #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: 2.26 Å3/Da / Density % sol: 45.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.1M Imidazole, 1.0-1.1K/Na tartrate, pH 7.8, 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-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 2002 / Details: Mirror |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. obs: 178663 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.301 / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XNB Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / SU B: 0.993 / SU ML: 0.04 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.066 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.159 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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