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- PDB-1qyd: Crystal structures of pinoresinol-lariciresinol and phenylcoumara... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qyd | ||||||
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Title | Crystal structures of pinoresinol-lariciresinol and phenylcoumaran benzylic ether reductases, and their relationship to isoflavone reductases | ||||||
![]() | pinoresinol-lariciresinol reductase | ||||||
![]() | PLANT PROTEIN / NADPH-dependent aromatic alcohol reductases / PCBER / PLR / IFR / lignans / isoflavonoids | ||||||
Function / homology | ![]() (-)-lariciresinol reductase / lariciresinol reductase activity / (-)-pinoresinol catabolic process / (+)-pinoresinol catabolic process / (-)-lariciresinol catabolic process / (-)-lariciresinol biosynthetic process / (+)-lariciresinol biosynthetic process / (+)-secoisolariciresinol biosynthetic process / (+)-pinoresinol reductase / (-)-pinoresinol reductase ...(-)-lariciresinol reductase / lariciresinol reductase activity / (-)-pinoresinol catabolic process / (+)-pinoresinol catabolic process / (-)-lariciresinol catabolic process / (-)-lariciresinol biosynthetic process / (+)-lariciresinol biosynthetic process / (+)-secoisolariciresinol biosynthetic process / (+)-pinoresinol reductase / (-)-pinoresinol reductase / lignan biosynthetic process / pinoresinol reductase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Min, T. / Kasahara, H. / Bedgar, D.L. / Youn, B. / Lawrence, P.K. / Gang, D.R. / Halls, S.C. / Park, H. / Hilsenbeck, J.L. / Davin, L.B. / Kang, C. | ||||||
![]() | ![]() Title: Crystal structures of pinoresinol-lariciresinol and phenylcoumaran benzylic ether reductases and their relationship to isoflavone reductases. Authors: Min, T. / Kasahara, H. / Bedgar, D.L. / Youn, B. / Lawrence, P.K. / Gang, D.R. / Halls, S.C. / Park, H. / Hilsenbeck, J.L. / 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 | ![]() | 252.2 KB | Display | ![]() |
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PDB format | ![]() | 205.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 395 KB | Display | ![]() |
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Full document | ![]() | 459.5 KB | Display | |
Data in XML | ![]() | 31.5 KB | Display | |
Data in CIF | ![]() | 47.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
#1: Protein | Mass: 35624.059 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.56 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 8000, MES, NaCl, Ca Acetate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→10 Å / Num. all: 33210 / Num. obs: 33210 / % possible obs: 79 % / Observed criterion σ(I): 0 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. measured all: 36439 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |