+Open data
-Basic information
Entry | Database: PDB / ID: 6lps | ||||||
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Title | Crystal structure of family 10 xylanase from Bacillus halodurans | ||||||
Components | Beta-xylanaseXylanase | ||||||
Keywords | HYDROLASE / GH10 xylanase from Bacillus halodurans | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus halodurans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21357153532 Å | ||||||
Authors | Xiang, L. / Zhang, G. / Zhou, J. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of family 10 xylanase from Bacillus halodurans Authors: Xiang, L. / Zhang, G. / Zhou, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lps.cif.gz | 110.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lps.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 6lps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/6lps ftp://data.pdbj.org/pub/pdb/validation_reports/lp/6lps | HTTPS FTP |
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-Related structure data
Related structure data | 2uwfS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 40952.934 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (bacteria) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q17TM8, endo-1,4-beta-xylanase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.33 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M Magnesium chloride, 0.1M Hepes pH 7, 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU R-AXIS / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→50 Å / Num. obs: 19247 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 27.6527547759 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 19.89 |
Reflection shell | Resolution: 2.21→2.25 Å / Redundancy: 6 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 8.02 / Rsym value: 0.219 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2UWF Resolution: 2.21357153532→39.1679388347 Å / SU ML: 0.233295999014 / Cross valid method: FREE R-VALUE / σ(F): 1.34754042894 / Phase error: 21.0810231913 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.3013295677 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21357153532→39.1679388347 Å
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Refine LS restraints |
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LS refinement shell |
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