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Open data
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Basic information
Entry | Database: PDB / ID: 2bgl | ||||||
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Title | X-Ray structure of binary-Secoisolariciresinol Dehydrogenase | ||||||
![]() | RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE | ||||||
![]() | XIDOREDUCTASE / ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Youn, B. / Moinuddin, S.G. / Davin, L.B. / Lewis, N.G. / Kang, C. | ||||||
![]() | ![]() Title: Crystal Structures of Apo-Form and Binary/Ternary Complexes of Podophyllum Secoisolariciresinol Dehydrogenase, an Enzyme Involved in Formation of Health-Protecting and Plant Defense Lignans Authors: Youn, B. / Moinuddin, S.G. / Davin, L.B. / Lewis, N.G. / Kang, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.9 KB | Display | ![]() |
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PDB format | ![]() | 48 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 324.8 KB | Display | ![]() |
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Full document | ![]() | 341.7 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bgkC ![]() 2bgmC ![]() 1bgkS C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components
#1: Protein | Mass: 29285.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NAJ / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.24 % |
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Crystal grow![]() | pH: 8.5 / Details: pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→50 Å / Num. obs: 5752 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.58 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.3 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1BGK Resolution: 2.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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