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Yorodumi- PDB-8wg1: Crystal structure of GH97 glucodextranase mutant E509Q from Flavo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wg1 | |||||||||
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Title | Crystal structure of GH97 glucodextranase mutant E509Q from Flavobacterium johnsoniae in complex with panose | |||||||||
Components | Candidate alpha-glucosidase Glycoside hydrolase family 97 | |||||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / GH97 / DEXTRAN / TIM-BARREL / ISOMALTOSE / NIGEROSE | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Flavobacterium johnsoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | |||||||||
Authors | Kurata, R. / Nakamura, S. / Miyazaki, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Febs J. / Year: 2024 Title: Structural insights into alpha-(1→6)-linkage preference of GH97 glucodextranase from Flavobacterium johnsoniae. Authors: Nakamura, S. / Kurata, R. / Miyazaki, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wg1.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8wg1.ent.gz | 891.3 KB | Display | PDB format |
PDBx/mmJSON format | 8wg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wg1_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8wg1_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8wg1_validation.xml.gz | 94.8 KB | Display | |
Data in CIF | 8wg1_validation.cif.gz | 132.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/8wg1 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/8wg1 | HTTPS FTP |
-Related structure data
Related structure data | 8wg0C 8wg2C 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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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 77769.805 Da / Num. of mol.: 4 / Mutation: E509Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101) (bacteria) Strain: ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101 Gene: Fjoh_4429 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5FBI0, glucan 1,6-alpha-glucosidase #2: Polysaccharide | alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 445 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.42 Å3/Da / Density % sol: 49.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 12% PEG20000, 200 mM sodium cacodylate buffer (pH 6.0), 200 mM magnesium acetate, 10 mM glucose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→49.23 Å / Num. obs: 132638 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.086 / Rrim(I) all: 0.227 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.34→2.38 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.347 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 89573 / CC1/2: 0.734 / Rpim(I) all: 0.542 / Rrim(I) all: 1.453 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→49.23 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.905 / SU B: 18.067 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.393 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.213 Å2
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Refinement step | Cycle: 1 / Resolution: 2.34→49.23 Å
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