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Yorodumi- PDB-1qyc: Crystal structures of pinoresinol-lariciresinol and phenylcoumara... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qyc | ||||||
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Title | Crystal structures of pinoresinol-lariciresinol and phenylcoumaran benzylic ether reductases, and their relationship to isoflavone reductases | ||||||
Components | phenylcoumaran benzylic ether reductase PT1 | ||||||
Keywords | PLANT PROTEIN / NADPH-dependent aromatic alcohol reductases / PCBER / PLR / IFR / lignans / isoflavonoids | ||||||
Function / homology | Function and homology information Oxidoreductases; Reducing C-O-C group as acceptor; With NADH or NADPH as donor / oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / lignan biosynthetic process Similarity search - Function | ||||||
Biological species | Pinus taeda (loblolly pine) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD, MIR / Resolution: 2.2 Å | ||||||
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. / Kang, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qyc.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qyc.ent.gz | 105 KB | Display | PDB format |
PDBx/mmJSON format | 1qyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/1qyc ftp://data.pdbj.org/pub/pdb/validation_reports/qy/1qyc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33563.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pinus taeda (loblolly pine) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9LL41 #2: Water | ChemComp-HOH / | |
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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: 2.28 Å3/Da / Density % sol: 45.94 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, Na cacodylate, Na citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 23, 2002 |
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→10 Å / Num. all: 26284 / Num. obs: 26284 / % possible obs: 98 % / Observed criterion σ(I): 0 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. measured all: 144316 |
-Processing
Software |
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Refinement | Method to determine structure: MAD, MIR / Resolution: 2.2→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å / Rfactor Rfree: 0.234 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |