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Yorodumi- PDB-6t0i: The wild type glucuronoyl esterase OtCE15A from Opitutus terrae i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t0i | |||||||||
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Title | The wild type glucuronoyl esterase OtCE15A from Opitutus terrae in complex with the aldotetrauronic acid XUX | |||||||||
Components | glucuronoyl esterase OtCE15A | |||||||||
Keywords | HYDROLASE / Esterase / Complex / Biomass | |||||||||
Function / homology | Alpha/Beta hydrolase fold / metal ion binding / : / DI(HYDROXYETHYL)ETHER / Putative acetyl xylan esterase Function and homology information | |||||||||
Biological species | Opitutus terrae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | |||||||||
Authors | Mazurkewich, S. / Navarro Poulsen, J.C. / Larsbrink, J. / Lo Leggio, L. | |||||||||
Funding support | Sweden, Denmark, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Structural and biochemical studies of the glucuronoyl esteraseOtCE15A illuminate its interaction with lignocellulosic components. Authors: Mazurkewich, S. / Poulsen, J.N. / Lo Leggio, L. / Larsbrink, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t0i.cif.gz | 173.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t0i.ent.gz | 133.5 KB | Display | PDB format |
PDBx/mmJSON format | 6t0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t0i_validation.pdf.gz | 821.7 KB | Display | wwPDB validaton report |
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Full document | 6t0i_full_validation.pdf.gz | 826.4 KB | Display | |
Data in XML | 6t0i_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 6t0i_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t0/6t0i ftp://data.pdbj.org/pub/pdb/validation_reports/t0/6t0i | HTTPS FTP |
-Related structure data
Related structure data | 6syrC 6syuC 6syvC 6sz0C 6sz4C 6szoC 6t0eC 6gs0S 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 46148.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Opitutus terrae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B1ZMF4, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases |
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#2: Polysaccharide | 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)- ...4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 277 molecules
#3: Chemical | ChemComp-MG / | ||||
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#4: Chemical | ChemComp-K / | ||||
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
-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 grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution E8: 0.12 M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M ...Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution E8: 0.12 M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol), 0.1 M Buffer System 2 pH 7.5 (Sodium HEPES; MOPS), and 50 % v/v Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350) |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→32.49 Å / Num. obs: 42551 / % possible obs: 88.56 % / Redundancy: 3.7 % / Biso Wilson estimate: 22.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04434 / Rpim(I) all: 0.02683 / Rrim(I) all: 0.05191 / Net I/σ(I): 15.38 |
Reflection shell | Resolution: 1.53→1.59 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 0.72 / Num. unique obs: 3634 / CC1/2: 0.508 / Rpim(I) all: 0.8103 / % possible all: 67.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6gs0 Resolution: 1.53→32.49 Å / SU ML: 0.266 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.8711
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→32.49 Å
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Refine LS restraints |
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LS refinement shell |
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