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- PDB-6syr: The wild type glucuronoyl esterase OtCE15A from Opitutus terrae i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6syr | |||||||||
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Title | The wild type glucuronoyl esterase OtCE15A from Opitutus terrae in complex with D-glucuronate | |||||||||
![]() | glucuronoyl esterase OtCE15A | |||||||||
![]() | HYDROLASE / Esterase / Complex / Biomass | |||||||||
Function / homology | Alpha/Beta hydrolase fold / metal ion binding / alpha-D-glucopyranuronic acid / Putative acetyl xylan esterase![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mazurkewich, S. / Navarro Poulsen, J.C. / Larsbrink, J. / Lo Leggio, L. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.7 KB | Display | ![]() |
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PDB format | ![]() | 128 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 787.8 KB | Display | ![]() |
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Full document | ![]() | 790.4 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6syuC ![]() 6syvC ![]() 6sz0C ![]() 6sz4C ![]() 6szoC ![]() 6t0eC ![]() 6t0iC ![]() 6gs0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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![](data/chem/img/GCU.gif)
![](data/chem/img/GCU.gif)
#1: Protein | Mass: 47844.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Sugar | ChemComp-GCU / |
-Non-polymers , 4 types, 233 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / | ||||
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#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Based on the Morpheus screen from Molecular Dimensions: G12 - 0.1 M Carboxylic acids, 0.1 M Buffer System 3, pH 8.5, 50 % v/v Precipitant Mix 4 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 0.918374 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→32.69 Å / Num. obs: 47249 / % possible obs: 91.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 21.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06132 / Rpim(I) all: 0.03731 / Rrim(I) all: 0.07189 / Net I/σ(I): 9.88 |
Reflection shell | Resolution: 1.49→1.543 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.416 / Mean I/σ(I) obs: 0.82 / Num. unique obs: 18505 / CC1/2: 0.656 / Rpim(I) all: 0.8315 / % possible all: 91.36 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6GS0 Resolution: 1.49→32.69 Å / SU ML: 0.2318 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.9957
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.49→32.69 Å
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Refine LS restraints |
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LS refinement shell |
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