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Yorodumi- PDB-7n6o: The crystal structure of the GH30 subfamily 10 enzyme, AcXbh30A f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n6o | ||||||
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Title | The crystal structure of the GH30 subfamily 10 enzyme, AcXbh30A from Acetivibrio clariflavus in complex with xylobiose | ||||||
Components | AcXbh30A | ||||||
Keywords | HYDROLASE / GH30 | ||||||
Function / homology | Function and homology information glucosylceramidase activity / sphingolipid metabolic process / polysaccharide catabolic process Similarity search - Function | ||||||
Biological species | Acetivibrio clariflavus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Tan, K. / St John, J.F. | ||||||
Citation | Journal: Febs Lett. / Year: 2022 Title: The first crystal structure of a xylobiose-bound xylobiohydrolase with high functional specificity from the bacterial glycoside hydrolase family 30, subfamily 10. Authors: St John, F.J. / Crooks, C. / Kim, Y. / Tan, K. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n6o.cif.gz | 375.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n6o.ent.gz | 303.6 KB | Display | PDB format |
PDBx/mmJSON format | 7n6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n6o_validation.pdf.gz | 1004.3 KB | Display | wwPDB validaton report |
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Full document | 7n6o_full_validation.pdf.gz | 1008.5 KB | Display | |
Data in XML | 7n6o_validation.xml.gz | 37.4 KB | Display | |
Data in CIF | 7n6o_validation.cif.gz | 56.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/7n6o ftp://data.pdbj.org/pub/pdb/validation_reports/n6/7n6o | HTTPS FTP |
-Related structure data
Related structure data | 7n6hSC S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 50078.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetivibrio clariflavus (bacteria) / Gene: Clocl_1795 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: G8LU16 #2: Polysaccharide | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.34 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 0.1M Sodium acetate 25% (w/v) PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2020 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→34.2 Å / Num. obs: 125373 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 12.3 Å2 / CC1/2: 0.986 / CC star: 0.997 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.069 / Rrim(I) all: 0.121 / Χ2: 2.06 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.946 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6128 / CC1/2: 0.442 / CC star: 0.783 / Rpim(I) all: 0.657 / Rrim(I) all: 1.157 / Χ2: 0.722 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7N6H Resolution: 1.5→34.2 Å / Cross valid method: FREE R-VALUE / σ(F): 18.24 / Phase error: 31.82 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→34.2 Å
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Refine LS restraints |
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LS refinement shell |
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