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- PDB-6syv: The glucuronoyl esterase OtCE15A S267A variant from Opitutus terr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6syv | |||||||||
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Title | The glucuronoyl esterase OtCE15A S267A variant from Opitutus terrae in complex with D-glucuronate | |||||||||
![]() | glucuronoyl esterase OtCE15A | |||||||||
![]() | HYDROLASE / Esterase / Complex / Biomass | |||||||||
Function / homology | Alpha/Beta hydrolase fold / metal ion binding / beta-D-glucopyranuronic acid / alpha-D-glucopyranuronic acid / DI(HYDROXYETHYL)ETHER / 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 | ![]() | 178.2 KB | Display | ![]() |
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PDB format | ![]() | 138.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 31.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6syrC ![]() 6syuC ![]() 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46132.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 2 molecules ![](data/chem/img/GCU.gif)
![](data/chem/img/BDP.gif)
![](data/chem/img/BDP.gif)
#4: Sugar | ChemComp-GCU / |
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#5: Sugar | ChemComp-BDP / |
-Non-polymers , 4 types, 383 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / | ||||
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#3: Chemical | ChemComp-EDO / #6: Chemical | #7: 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 | Density Matthews: 1.82 Å3/Da / Density % sol: 32.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution G12: 0.1 M Carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; ...Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution G12: 0.1 M Carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1 M Buffer System 3 pH 8.5 (Tris; BICINE), and 50 % v/v Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873127 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→36.22 Å / Num. obs: 102117 / % possible obs: 81.67 % / Redundancy: 3.3 % / Biso Wilson estimate: 13.27 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.08792 / Rpim(I) all: 0.05606 / Rrim(I) all: 0.1046 / Net I/σ(I): 6.12 |
Reflection shell | Resolution: 1.12→1.16 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.044 / Mean I/σ(I) obs: 0.76 / Num. unique obs: 4777 / CC1/2: 0.452 / Rpim(I) all: 0.6856 / Rrim(I) all: 1.255 / % possible all: 38.26 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6gs0 Resolution: 1.12→36.22 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.307
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→36.22 Å
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Refine LS restraints |
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LS refinement shell |
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