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Yorodumi- PDB-6sz4: The glucuronoyl esterase OtCE15A H408A variant from Opitutus terr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sz4 | |||||||||
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Title | The glucuronoyl esterase OtCE15A H408A variant from Opitutus terrae in complex with, and covalently linked to, D-glucuronate | |||||||||
Components | glucuronoyl esterase OtCE15A | |||||||||
Keywords | HYDROLASE / Esterase / Complex / Biomass | |||||||||
Function / homology | Alpha/Beta hydrolase fold / beta-D-glucopyranuronic acid / FORMIC ACID / Putative acetyl xylan esterase Function and homology information | |||||||||
Biological species | Opitutus terrae PB90-1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 | 6sz4.cif.gz | 159.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sz4.ent.gz | 123 KB | Display | PDB format |
PDBx/mmJSON format | 6sz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/6sz4 ftp://data.pdbj.org/pub/pdb/validation_reports/sz/6sz4 | HTTPS FTP |
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-Related structure data
Related structure data | 6syrC 6syuC 6syvC 6sz0C 6szoC 6t0eC 6t0iC 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
#1: Protein | Mass: 46081.480 Da / Num. of mol.: 1 / Mutation: H408A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Opitutus terrae PB90-1 (bacteria) / Gene: Oter_0116 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1ZMF4 |
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#2: Sugar | ChemComp-BDP / |
#3: Chemical | ChemComp-FMT / |
#4: 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 grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: Protein mixed 50/50 with reservoir solution of 0.2 M Ammonium formate None 20 % 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: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.749→45.56 Å / Num. obs: 30662 / % possible obs: 95.48 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.59 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.09829 / Rpim(I) all: 0.06242 / Rrim(I) all: 0.1169 / Net I/σ(I): 6.62 |
Reflection shell | Resolution: 1.749→1.812 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.8285 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 2844 / CC1/2: 0.736 / Rpim(I) all: 0.5228 / Rrim(I) all: 0.9829 / % possible all: 88.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6gs0 Resolution: 1.75→45.56 Å / SU ML: 0.258 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 38.9229
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→45.56 Å
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Refine LS restraints |
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LS refinement shell |
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