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Yorodumi- PDB-6rv7: Crystal Structure of Glucuronoyl Esterase from Cerrena unicolor i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rv7 | |||||||||
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Title | Crystal Structure of Glucuronoyl Esterase from Cerrena unicolor inactive S270A variant in complex with the aldouronic acid UXXR | |||||||||
Components | 4-O-methyl-glucuronoyl methylesterase | |||||||||
Keywords | HYDROLASE / CE15 / esterase / alpha/beta-hydrolase / ligand-bound | |||||||||
Function / homology | Function and homology information (4-O-methyl)-D-glucuronate-lignin esterase / lignin catabolic process / carboxylic ester hydrolase activity / cellulose binding / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Cerrena unicolor (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å | |||||||||
Model details | S270A variant in complex with the aldouronic acid Um4X | |||||||||
Authors | Ernst, H.A. / Mosbech, C. / Langkilde, A. / Westh, P. / Meyer, A. / Agger, J.W. / Larsen, S. | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: The structural basis of fungal glucuronoyl esterase activity on natural substrates. Authors: Ernst, H.A. / Mosbech, C. / Langkilde, A.E. / Westh, P. / Meyer, A.S. / Agger, J.W. / Larsen, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rv7.cif.gz | 310.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rv7.ent.gz | 249.1 KB | Display | PDB format |
PDBx/mmJSON format | 6rv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rv7_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6rv7_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6rv7_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 6rv7_validation.cif.gz | 49 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/6rv7 ftp://data.pdbj.org/pub/pdb/validation_reports/rv/6rv7 | HTTPS FTP |
-Related structure data
Related structure data | 6rtvSC 6ru1C 6ru2C 6rv8C 6rv9C 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43210.930 Da / Num. of mol.: 2 / Mutation: S270A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cerrena unicolor (fungus) / Plasmid: pPICZ-alpha / Production host: Komagataella pastoris (fungus) / Variant (production host): X-33 References: UniProt: A0A0A7EQR3, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-Xylitol Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose |
#4: Sugar |
-Non-polymers , 2 types, 519 molecules
#5: Chemical | ChemComp-EDO / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M phosphate-citrate pH 4.2, 0.1 M KCl, 20% w/v PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99987 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.73→49.33 Å / Num. obs: 99913 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 20.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.049 / Rrim(I) all: 0.129 / Net I/σ(I): 10.3 / Num. measured all: 686893 / Scaling rejects: 39 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RTV Resolution: 1.73→49.327 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.39 Å2 / Biso mean: 23.6803 Å2 / Biso min: 11.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.73→49.327 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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