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Yorodumi- PDB-2dck: A tetragonal-lattice structure of alkaliphilic XynJ from Bacillus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dck | ||||||
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Title | A tetragonal-lattice structure of alkaliphilic XynJ from Bacillus sp. 41M-1 | ||||||
Components | xylanase J | ||||||
Keywords | HYDROLASE / family 11 / Xylan Binding Domain (XBM) / beta-jelly roll / alkaliphilic xylanase | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Fibriansah, G. / Ihsanawati / Tanaka, N. / Nakamura, S. / Kumasaka, T. | ||||||
Citation | Journal: To be Published Title: A two-domain structure of alkaliphilic XynJ from Bacillus sp. 41M-1 Authors: Ihsanawati / Tanaka, N. / Nakamura, S. / Kumasaka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dck.cif.gz | 87.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dck.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 2dck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/2dck ftp://data.pdbj.org/pub/pdb/validation_reports/dc/2dck | HTTPS FTP |
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-Related structure data
Related structure data | 2dcjSC 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: 39027.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: 41M-1 / Gene: xynJ / Plasmid: pUC119 / Production host: Escherichia coli (E. coli) References: GenBank: 5381269, UniProt: Q9RC94*PLUS, endo-1,4-beta-xylanase | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 69.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10mM sodium phosphate buffer (Na2HPO4/NaH2PO4), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 24, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→119.52 Å / Num. obs: 36572 / % possible obs: 99.9 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DCJ Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.209 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.121 / 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: 27.456 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.096→2.15 Å / Total num. of bins used: 20 /
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