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Yorodumi- PDB-8hdd: Complex structure of catalytic, small, and a partial electron tra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hdd | ||||||
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Title | Complex structure of catalytic, small, and a partial electron transfer subunits from Burkholderia cepacia FAD glucose dehydrogenase | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Glucose dehydrogenase / FAD / Burkholderia cepacia / cytochrome c / HEM | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding / electron transfer activity / iron ion binding / heme binding / plasma membrane Similarity search - Function | ||||||
Biological species | Burkholderia cepacia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Yoshida, H. / Sode, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Commun Biol / Year: 2022 Title: Microgravity environment grown crystal structure information based engineering of direct electron transfer type glucose dehydrogenase. Authors: Okuda-Shimazaki, J. / Yoshida, H. / Lee, I. / Kojima, K. / Suzuki, N. / Tsugawa, W. / Yamada, M. / Inaka, K. / Tanaka, H. / Sode, K. #1: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein. Authors: Yoshida, H. / Kojima, K. / Shiota, M. / Yoshimatsu, K. / Yamazaki, T. / Ferri, S. / Tsugawa, W. / Kamitori, S. / Sode, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hdd.cif.gz | 332.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hdd.ent.gz | 260.7 KB | Display | PDB format |
PDBx/mmJSON format | 8hdd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/8hdd ftp://data.pdbj.org/pub/pdb/validation_reports/hd/8hdd | HTTPS FTP |
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-Related structure data
Related structure data | 6a2uS S: Starting model for refinement |
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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
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 59906.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GB:AAN39686.1 / Source: (gene. exp.) Burkholderia cepacia (bacteria) / Gene: gdhAlpha / Plasmid: pTrc99A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8GQE7, EC: 1.1.5.9 |
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#2: Protein | Mass: 51796.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GB:AAQ06608.1 / Source: (gene. exp.) Burkholderia cepacia (bacteria) / Plasmid: plasmid / Details (production host): pTrc99A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q71JE9 |
#3: Protein | Mass: 13053.861 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GB:CAZ78686.1 / Source: (gene. exp.) Burkholderia cepacia (bacteria) / Gene: BMULJ_04411 / Plasmid: plasmid / Details (production host): pTrc99A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3KLY3 |
-Non-polymers , 3 types, 3 molecules
#4: Chemical | ChemComp-FAD / |
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#5: Chemical | ChemComp-F3S / |
#6: Chemical | ChemComp-HEM / |
-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: 3.5 Å3/Da / Density % sol: 64.9 % |
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Crystal grow | Temperature: 293 K / Method: counter-diffusion / pH: 5.6 / Details: tacsimate, PEG 3350, DDM, sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 34334 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.165 / Rrim(I) all: 0.179 / Net I/σ(I): 10.34 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6A2U Resolution: 3→49.88 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.876 / SU B: 94.265 / SU ML: 0.633 / Cross valid method: THROUGHOUT / ESU R Free: 0.425 / 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: 74.33 Å2
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Refinement step | Cycle: 1 / Resolution: 3→49.88 Å
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Refine LS restraints |
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