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- PDB-6jwf: Holo form of Pyranose Dehydrogenase PQQ domain from Coprinopsis c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jwf | ||||||
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Title | Holo form of Pyranose Dehydrogenase PQQ domain from Coprinopsis cinerea | ||||||
![]() | Extracellular PQQ-dependent sugar dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / pyrroloquinoline quinone / sugar dehydrogenase / AA family 12 | ||||||
Function / homology | ![]() cellulose binding / cellulose catabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Takeda, K. / Ishida, T. / Yoshida, M. / Samejima, M. / Ohno, H. / Igarashi, K. / Nakamura, N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of the Catalytic and CytochromebDomains in a Eukaryotic Pyrroloquinoline Quinone-Dependent Dehydrogenase. Authors: Takeda, K. / Ishida, T. / Yoshida, M. / Samejima, M. / Ohno, H. / Igarashi, K. / Nakamura, N. #1: ![]() Title: The first crystal structure of the catalytic domain and the cytochrome b domain in a eukaryotic PQQ-dependent dehydrogenase Authors: Takeda, K. / Ishida, T. / Yoshida, M. / Samejima, M. / Ohno, H. / Igarashi, K. / Nakamura, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 221 KB | Display | ![]() |
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PDB format | ![]() | 173.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6jt5SC ![]() 6jt6C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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, 3 molecules AB![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 45173.996 Da / Num. of mol.: 2 / Fragment: PQQ dependent catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #6: Sugar | ChemComp-NAG / | |
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-Non-polymers , 5 types, 1537 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/PQQ.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PQQ.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.71 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 5 / Details: 5mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→100 Å / Num. obs: 213104 / % possible obs: 99.4 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.3→1.38 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.99 / Num. unique obs: 33130 / CC1/2: 0.863 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JT5 Resolution: 1.3→71.07 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.3→71.07 Å
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LS refinement shell | Resolution: 1.297→1.33 Å / Total num. of bins used: 20
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