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Yorodumi- PDB-6jr7: Flavobacterium johnsoniae GH31 dextranase, FjDex31A, complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jr7 | |||||||||
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Title | Flavobacterium johnsoniae GH31 dextranase, FjDex31A, complexed with glucose | |||||||||
Components | Candidate alpha-glycosidase Glycoside hydrolase family 31 | |||||||||
Keywords | HYDROLASE / dextranase / Flavobacterium johnsoniae / dextran / isomaltose / GH31 | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Flavobacterium johnsoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Tonozuka, T. | |||||||||
Funding support | Japan, 1items
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Citation | Journal: Febs J. / Year: 2020 Title: Structural insights into polysaccharide recognition by Flavobacterium johnsoniae dextranase, a member of glycoside hydrolase family 31. Authors: Tsutsumi, K. / Gozu, Y. / Nishikawa, A. / Tonozuka, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jr7.cif.gz | 732.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jr7.ent.gz | 588.3 KB | Display | PDB format |
PDBx/mmJSON format | 6jr7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jr7_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6jr7_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6jr7_validation.xml.gz | 138.6 KB | Display | |
Data in CIF | 6jr7_validation.cif.gz | 213.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/6jr7 ftp://data.pdbj.org/pub/pdb/validation_reports/jr/6jr7 | HTTPS FTP |
-Related structure data
Related structure data | 6jr6SC 6jr8C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 96182.477 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / UW101) (bacteria) Strain: ATCC 17061 / DSM 2064 / UW101 / Gene: Fjoh_4430 / Production host: Escherichia coli (E. coli) / References: UniProt: A5FBI1, alpha-glucosidase #2: Polysaccharide | alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-MPD / ( #5: Water | ChemComp-HOH / | |
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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: 2.91 Å3/Da / Density % sol: 57.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM sodium acetate buffer, 8% (w/v) polyethylene glycol 20000, and 8% 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→35.2 Å / Num. obs: 430825 / % possible obs: 94.8 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 19944 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JR6 Resolution: 1.75→35.15 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Leu308-Gln309 adopts a cis conformation yet the electron density is clearly seen. Two glucose molecules are found as a continuous electron density map, which can be modeled as an isomaltose ...Details: Leu308-Gln309 adopts a cis conformation yet the electron density is clearly seen. Two glucose molecules are found as a continuous electron density map, which can be modeled as an isomaltose molecule. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.65 Å2 / Biso mean: 23.002 Å2 / Biso min: 11.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→35.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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