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Yorodumi- PDB-7toh: Crystal structure of carbohydrate esterase PbeAcXE, in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7toh | ||||||
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Title | Crystal structure of carbohydrate esterase PbeAcXE, in complex with MeGlcpA-Xylp | ||||||
Components | SGNH hydrolase | ||||||
Keywords | HYDROLASE / carbohydrate esterase / CE / Acetyl xylan esterases / xylan esterase / AcXE | ||||||
Function / homology | SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / hydrolase activity / SGNH hydrolase Function and homology information | ||||||
Biological species | Prolixibacter bellariivorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.26 Å | ||||||
Authors | Stogios, P.J. / Skarina, T. / Di Leo, R. / Jurak, E. / Master, E. | ||||||
Funding support | 1items
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Citation | Journal: Molecules / Year: 2022 Title: Elucidating Sequence and Structural Determinants of Carbohydrate Esterases for Complete Deacetylation of Substituted Xylans. Authors: Penttinen, L. / Kouhi, V. / Faure, R. / Skarina, T. / Stogios, P. / Master, E. / Jurak, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7toh.cif.gz | 215.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7toh.ent.gz | 154.2 KB | Display | PDB format |
PDBx/mmJSON format | 7toh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7toh_validation.pdf.gz | 448.5 KB | Display | wwPDB validaton report |
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Full document | 7toh_full_validation.pdf.gz | 449.2 KB | Display | |
Data in XML | 7toh_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 7toh_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/7toh ftp://data.pdbj.org/pub/pdb/validation_reports/to/7toh | HTTPS FTP |
-Related structure data
Related structure data | 7togC 7toiC 7tojC 7tokC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42729.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Prolixibacter bellariivorans (bacteria) Gene: PbJCM13498_02590 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic / References: UniProt: A0A5M4AV20 |
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#2: Polysaccharide | 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose Type: oligosaccharide / Mass: 340.281 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: 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 | Density Matthews: 2.12 Å3/Da / Density % sol: 42.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20 mM acetylated xylooligosaccharides, 0.1 M Tris pH 6.5 and 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→28.53 Å / Num. obs: 93487 / % possible obs: 97.4 % / Redundancy: 11.8 % / Biso Wilson estimate: 16.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.03 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.26→1.29 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.467 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6513 / CC1/2: 0.557 / Rpim(I) all: 0.583 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.26→28.53 Å / SU ML: 0.1258 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.1006 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.26→28.53 Å
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Refine LS restraints |
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LS refinement shell |
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