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- PDB-6t0e: 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: 6t0e | |||||||||
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Title | The glucuronoyl esterase OtCE15A S267A variant from Opitutus terrae in complex with benzyl D-glucuronoate and D-glucuronate | |||||||||
![]() | glucuronoyl esterase OtCE15A | |||||||||
![]() | HYDROLASE / Esterase / Complex / Biomass | |||||||||
Function / homology | Alpha/Beta hydrolase fold / metal ion binding / alpha-D-glucopyranuronic acid / benzyl alpha-D-glucopyranuronate / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / trimethylamine oxide / 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 | ![]() | 327.1 KB | Display | ![]() |
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PDB format | ![]() | 266 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 36.9 KB | Display | |
Data in CIF | ![]() | 53 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6syrC ![]() 6syuC ![]() 6syvC ![]() 6sz0C ![]() 6sz4C ![]() 6szoC ![]() 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46132.547 Da / Num. of mol.: 2 / Mutation: S267A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 11246 / JCM 15787 / PB90-1 / Gene: Oter_0116 / Production host: ![]() ![]() |
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-Sugars , 2 types, 3 molecules ![](data/chem/img/GCU.gif)
![](data/chem/img/M55.gif)
![](data/chem/img/M55.gif)
#2: Sugar | #4: Sugar | ChemComp-M55 / | |
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-Non-polymers , 9 types, 472 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/TMO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/TMO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CL / | ||||||||||||
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#5: Chemical | ChemComp-PG4 / | ||||||||||||
#6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-PEG / #8: Chemical | ChemComp-PGE / #9: Chemical | ChemComp-MG / | #10: Chemical | ChemComp-TMO / #11: Chemical | ChemComp-DMS / #12: 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: 2.14 Å3/Da / Density % sol: 42.39 % |
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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 JCSG+ screen solution G4: 0.2 M Trimethylamine N-oxide, 0.1 M Tris pH 8.5, and 20 % w/v PEG 2000 MME |
-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: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→44.45 Å / Num. obs: 63514 / % possible obs: 98.98 % / Redundancy: 13.6 % / Biso Wilson estimate: 33.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1589 / Rpim(I) all: 0.04436 / Rrim(I) all: 0.1651 / Net I/σ(I): 12.25 |
Reflection shell | Resolution: 1.89→1.96 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 0.84 / Num. unique obs: 5944 / CC1/2: 0.403 / Rpim(I) all: 0.6206 / % possible all: 92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6gs0 Resolution: 1.89→44.45 Å / SU ML: 0.2534 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.5575
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→44.45 Å
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Refine LS restraints |
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LS refinement shell |
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