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Yorodumi- PDB-6xn2: Crystal structure of the GH43_1 enzyme from Xanthomonas citri com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xn2 | |||||||||
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Title | Crystal structure of the GH43_1 enzyme from Xanthomonas citri complexed with xylotriose | |||||||||
Components | Xylosidase | |||||||||
Keywords | HYDROLASE / glycoside hydrolase / GH43 | |||||||||
Function / homology | Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / 4beta-beta-xylotriose / DI(HYDROXYETHYL)ETHER / beta-D-xylopyranose / Xylosidase Function and homology information | |||||||||
Biological species | Xanthomonas axonopodis pv. citri (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.652 Å | |||||||||
Authors | Morais, M.A.B. / Tonoli, C.C.C. / Santos, C.R. / Murakami, M.T. | |||||||||
Funding support | Brazil, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations. Authors: Morais, M.A.B. / Coines, J. / Domingues, M.N. / Pirolla, R.A.S. / Tonoli, C.C.C. / Santos, C.R. / Correa, J.B.L. / Gozzo, F.C. / Rovira, C. / Murakami, M.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xn2.cif.gz | 159.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xn2.ent.gz | 121.3 KB | Display | PDB format |
PDBx/mmJSON format | 6xn2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/6xn2 ftp://data.pdbj.org/pub/pdb/validation_reports/xn/6xn2 | HTTPS FTP |
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-Related structure data
Related structure data | 6xn0C 6xn1C 4mlgS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40225.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas axonopodis pv. citri (strain 306) (bacteria) Strain: 306 / Gene: xsa, XAC4258 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PET2 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose |
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#4: Sugar | ChemComp-XYP / |
-Non-polymers , 4 types, 515 molecules
#3: Chemical | #5: Chemical | ChemComp-PEG / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.6 Å3/Da / Density % sol: 52.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion Details: 0.2 M ammonium sulfate, 30% (w/v) Polietilenoglicol 8,000, 0.1 M sodium cacodylate pH 6.5 and 10 % glycerol |
-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: 1.459 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 2, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.459 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→29.413 Å / Num. obs: 63992 / % possible obs: 63.6 % / Redundancy: 4.343 % / Biso Wilson estimate: 30.13 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.057 / Χ2: 0.948 / Net I/σ(I): 16.58 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MLG Resolution: 1.652→29.41 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.33 / 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: 98.38 Å2 / Biso mean: 34.45 Å2 / Biso min: 21.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.652→29.41 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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