[English] 日本語
Yorodumi- PDB-6szo: The glucuronoyl esterase OtCE15A S267A variant from Opitutus terr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6szo | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The glucuronoyl esterase OtCE15A S267A variant from Opitutus terrae in complex with D-galacturonate | |||||||||
Components | glucuronoyl esterase OtCE15A | |||||||||
Keywords | HYDROLASE / Esterase / Complex / Biomass | |||||||||
Function / homology | Alpha/Beta hydrolase fold / metal ion binding / beta-D-galactopyranuronic acid / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Putative acetyl xylan esterase Function and homology information | |||||||||
Biological species | Opitutus terrae PB90-1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Mazurkewich, S. / Navarro Poulsen, J.C. / Larsbrink, J. / Lo Leggio, L. | |||||||||
Funding support | Sweden, Denmark, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6szo.cif.gz | 159.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6szo.ent.gz | 124.1 KB | Display | PDB format |
PDBx/mmJSON format | 6szo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6szo_validation.pdf.gz | 847.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6szo_full_validation.pdf.gz | 852.7 KB | Display | |
Data in XML | 6szo_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 6szo_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/6szo ftp://data.pdbj.org/pub/pdb/validation_reports/sz/6szo | HTTPS FTP |
-Related structure data
Related structure data | 6syrC 6syuC 6syvC 6sz0C 6sz4C 6t0eC 6t0iC 6gs0S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 46132.547 Da / Num. of mol.: 1 / Mutation: S267A 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 |
---|---|
#2: Sugar | ChemComp-GTR / |
-Non-polymers , 6 types, 159 molecules
#3: Chemical | ChemComp-DMS / #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PEG / #7: Chemical | ChemComp-PGE / #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.92 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution E8: 0.12 M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M ...Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution E8: 0.12 M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol), 0.1 M Buffer System 2 pH 7.5 (Sodium HEPES; MOPS), 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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9891 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9891 Å / Relative weight: 1 |
Reflection | Resolution: 2.198→44.74 Å / Num. obs: 16711 / % possible obs: 97.04 % / Redundancy: 2.7 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.08127 / Rpim(I) all: 0.05835 / Rrim(I) all: 0.1006 / Net I/σ(I): 8.66 |
Reflection shell | Resolution: 2.198→2.277 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4798 / Mean I/σ(I) obs: 2 / Num. unique obs: 1620 / CC1/2: 0.747 / Rpim(I) all: 0.3448 / Rrim(I) all: 0.594 / % possible all: 94.62 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6gs0 Resolution: 2.2→44.74 Å / SU ML: 0.2418 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.5455
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→44.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|