+Open data
-Basic information
Entry | Database: PDB / ID: 6tkx | |||||||||
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Title | Carbohydrate esterase from gut microbiota | |||||||||
Components | Carbohydrate esterase | |||||||||
Keywords | HYDROLASE / Carbohydrate esterase / alpha/beta hydrolase | |||||||||
Biological species | metagenome (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | |||||||||
Authors | Penttinen, L. / Hakulinen, N. / Master, R.E. | |||||||||
Funding support | Finland, Sweden, 2items
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Citation | Journal: Biotechnol Biofuels / Year: 2021 Title: Polysaccharide utilization loci-driven enzyme discovery reveals BD-FAE: a bifunctional feruloyl and acetyl xylan esterase active on complex natural xylans. Authors: Hameleers, L. / Penttinen, L. / Ikonen, M. / Jaillot, L. / Faure, R. / Terrapon, N. / Deuss, P.J. / Hakulinen, N. / Master, E.R. / Jurak, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tkx.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tkx.ent.gz | 90 KB | Display | PDB format |
PDBx/mmJSON format | 6tkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tkx_validation.pdf.gz | 433.8 KB | Display | wwPDB validaton report |
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Full document | 6tkx_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 6tkx_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 6tkx_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/6tkx ftp://data.pdbj.org/pub/pdb/validation_reports/tk/6tkx | HTTPS FTP |
-Related structure data
Related structure data | 6xycC 2c7bS 2wtmS 3bjrS 3bxpS 3f67S 3hxkS 3pfbS 3qh4S 3zwqS 4e15S 4n5hS 4q3kS 4v2iS 4wy8S 4zi5S 5ao9S 5cmlS 5g5cS 5jd4S 5l2pS 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: 32548.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-SO4 / |
#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: 2.1 Å3/Da / Density % sol: 41.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.2 M Ammonium sulfate, 25% PEG MME 5000, 0.1 M mes pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→41.399 Å / Num. obs: 17093 / % possible obs: 99.9 % / Redundancy: 8.7 % / CC1/2: 0.6 / Rrim(I) all: 0.143 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.06→2.1 Å / Num. unique obs: 838 / CC1/2: 0.6 / Rrim(I) all: 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HXK, 4N5H, 5AO9, 2WTM, 3BXP, 3BJR, 4V2I, 2C7B, 4E15, 4Q3K, 3PFB, 3ZWQ, 5L2P, 3QH4, 5G5C, 5JD4, 4ZI5, 3F67, 5CML, 4WY8 Resolution: 2.06→41.399 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→41.399 Å
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Refine LS restraints |
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LS refinement shell |
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