+Open data
-Basic information
Entry | Database: PDB / ID: 7d88 | ||||||
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Title | Crystal structure of a novel thermostable GH10 xylanase XynA | ||||||
Components | Beta-xylanaseXylanase | ||||||
Keywords | HYDROLASE / GH10 family / Thermostable / Bifunctional. | ||||||
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 sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34482019351 Å | ||||||
Authors | Xie, W. / Yu, Q. / Wang, C. | ||||||
Citation | Journal: Biochemistry / Year: 2021 Title: Insights into the Catalytic Mechanism of a Novel XynA and Structure-Based Engineering for Improving Bifunctional Activities. Authors: Xie, W. / Yu, Q. / Zhang, R. / Liu, Y. / Cao, R. / Wang, S. / Zhan, R. / Liu, Z. / Wang, K. / Wang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d88.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d88.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 7d88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/7d88 ftp://data.pdbj.org/pub/pdb/validation_reports/d8/7d88 | HTTPS FTP |
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-Related structure data
Related structure data | 7d89C 1v0lS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 49922.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: KW1 / Gene: xyn10A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P8ESF9, endo-1,4-beta-xylanase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 29% PEG 600 (w/v), 0.1 M CaCl2, 0.1 M MES pH 6.0 / PH range: 7.0-9.0 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→15.33 Å / Num. obs: 22405 / % possible obs: 99.35 % / Redundancy: 25.3 % / Biso Wilson estimate: 51.0611188386 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.031 / Rrim(I) all: 0.159 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.345→2.429 Å / Num. unique obs: 22405 / CC1/2: 0.99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V0L Resolution: 2.34482019351→15.3263372188 Å / SU ML: 0.24062012499 / Cross valid method: FREE R-VALUE / σ(F): 1.37661057842 / Phase error: 24.5715151416 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.7565312641 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34482019351→15.3263372188 Å
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Refine LS restraints |
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LS refinement shell |
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