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Yorodumi- PDB-8wg0: Crystal structure of GH97 glucodextranase from Flavobacterium joh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wg0 | |||||||||
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Title | Crystal structure of GH97 glucodextranase from Flavobacterium johnsoniae in complex with glucose | |||||||||
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: 1.95 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 | 8wg0.cif.gz | 2.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8wg0.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 8wg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wg0_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 8wg0_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 8wg0_validation.xml.gz | 98.6 KB | Display | |
Data in CIF | 8wg0_validation.cif.gz | 141 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/8wg0 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/8wg0 | HTTPS FTP |
-Related structure data
Related structure data | 8wg1C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: SER / Beg label comp-ID: SER / Auth asym-ID: A / Label asym-ID: A
NCS ensembles :
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-Components
#1: Protein | Mass: 80531.977 Da / Num. of mol.: 4 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: Chemical | ChemComp-CA / #3: Sugar | ChemComp-GLC / #4: Chemical | ChemComp-EDO / #5: 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: 2.37 Å3/Da / Density % sol: 48.12 % |
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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: AR-NW12A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→49.13 Å / Num. obs: 223030 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.471 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10951 / CC1/2: 0.836 / Rpim(I) all: 0.594 / Rrim(I) all: 1.588 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→49.13 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.284 / SU ML: 0.139 / Cross valid method: FREE R-VALUE / ESU R: 0.163 / ESU R Free: 0.149 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.206 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→49.13 Å
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