+Open data
-Basic information
Entry | Database: PDB / ID: 6wqw | ||||||||||||
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Title | Thermobacillus composti GH10 xylanase | ||||||||||||
Components | Beta-xylanase | ||||||||||||
Keywords | HYDROLASE / GH 10 / Glycoside Hydrolase / Thermobacillus composti | ||||||||||||
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 | Thermobacillus composti (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.102 Å | ||||||||||||
Authors | Briganti, L. / Polikarpov, I. | ||||||||||||
Funding support | Brazil, 3items
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Citation | Journal: Carbohydr Polym / Year: 2020 Title: Transformation of xylan into value-added biocommodities using Thermobacillus composti GH10 xylanase. Authors: Sepulchro, A.G.V. / Pellegrini, V.O.A. / Briganti, L. / de Araujo, E.A. / de Araujo, S.S. / Polikarpov, I. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wqw.cif.gz | 142.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wqw.ent.gz | 110.5 KB | Display | PDB format |
PDBx/mmJSON format | 6wqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wqw_validation.pdf.gz | 777.4 KB | Display | wwPDB validaton report |
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Full document | 6wqw_full_validation.pdf.gz | 779.9 KB | Display | |
Data in XML | 6wqw_validation.xml.gz | 14 KB | Display | |
Data in CIF | 6wqw_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/6wqw ftp://data.pdbj.org/pub/pdb/validation_reports/wq/6wqw | HTTPS FTP |
-Related structure data
Related structure data | 1n82S 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
#1: Protein | Mass: 38594.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobacillus composti (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: L0EGW1, endo-1,4-beta-xylanase |
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#2: Sugar | ChemComp-XYP / |
#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: 1.98 Å3/Da / Density % sol: 37.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, 70% (v/v) 2-Methyl-2,4-pentanediol (MPD) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 |
Reflection | Resolution: 2.102→33.82 Å / Num. obs: 18595 / % possible obs: 98.4 % / Redundancy: 22.7 % / CC1/2: 1 / Net I/σ(I): 18.26 |
Reflection shell | Resolution: 2.102→2.18 Å / Redundancy: 19.4 % / Mean I/σ(I) obs: 2.23 / Num. unique obs: 1809 / CC1/2: 0.868 / % possible all: 99.78 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N82 Resolution: 2.102→33.819 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.13 / Stereochemistry target values: ML
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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 max: 109.23 Å2 / Biso mean: 48.2512 Å2 / Biso min: 16.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.102→33.819 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 54.044 Å / Origin y: 25.2786 Å / Origin z: 47.0567 Å
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Refinement TLS group | Selection details: (chain A and resseq 4:330) |