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- PDB-1gp6: Anthocyanidin synthase from Arabidopsis thaliana complexed with t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gp6 | ||||||
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Title | Anthocyanidin synthase from Arabidopsis thaliana complexed with trans-dihydroquercetin (with 30 min exposure to O2) | ||||||
![]() | LEUCOANTHOCYANIDIN DIOXYGENASE![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wilmouth, R.C. / Turnbull, J.J. / Welford, R.W.D. / Clifton, I.J. / Prescott, A.G. / Schofield, C.J. | ||||||
![]() | ![]() Title: Structure and Mechanism of Anthocyanidin Synthase from Arabidopsis Thaliana. Authors: Wilmouth, R.C. / Turnbull, J.J. / Welford, R.W.D. / Clifton, I.J. / Prescott, A.G. / Schofield, C.J. #1: ![]() Title: Are Anthocyanidins the Immediate Products of Anthocyanidin Synthase? Authors: Turnbull, J.J. / Sobey, W.J. / Aplin, R.T. / Hassan, A. / Firmin, J.L. / Schofield, C.J. / Prescott, A.G. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Purification, Crystallization and Preliminary X-Ray Diffraction of Anthocyanidin Synthase from Arabidopsis Thaliana Authors: Turnbull, J.J. / Prescott, A.G. / Schofield, C.J. / Wilmouth, R.C. #3: Journal: Plant J. / Year: 1999 Title: Direct Evidence for Anthocyanidin Synthase as a 2-Oxoglutarate-Dependent Oxygenase: Molecular Cloning and Functional Expression of Cdna from a Red Forma of Perilla Frutescens Authors: Saito, K. / Kobayashi, M. / Gong, Z. / Tanaka, Y. / Yamazaki, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.6 KB | Display | ![]() |
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PDB format | ![]() | 69.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1gp4SC ![]() 1gp5C 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 40451.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 363 molecules ![](data/chem/img/SIN.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/QUE.gif)
![](data/chem/img/DH2.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/QUE.gif)
![](data/chem/img/DH2.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SIN / ![]() | ||||||||
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#3: Chemical | ![]() #4: Chemical | ChemComp-QUE / | ![]() #5: Chemical | ChemComp-DH2 / ( | #6: Chemical | ChemComp-FE2 / | #7: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.1 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | pH: 6.5 Details: 18% (W/V) PEG 2000 MONOMETHYLETHER, 50 MM MES, 200 MM AMMONIUM ACETATE, 2 MM IRON(II) SULPHATE, 10 MM POTASSIUM ALPHA-KETOGLUTARATE, 10 MM SODIUM ASCORBATE 10 MM DHQ (IN MEOH TO GIVE A FINAL ...Details: 18% (W/V) PEG 2000 MONOMETHYLETHER, 50 MM MES, 200 MM AMMONIUM ACETATE, 2 MM IRON(II) SULPHATE, 10 MM POTASSIUM ALPHA-KETOGLUTARATE, 10 MM SODIUM ASCORBATE 10 MM DHQ (IN MEOH TO GIVE A FINAL CONC. OF 10%(V/V) MEOH), PH 6.5, ANAEROBIC (AR ATMOSPHERE, < 0.5 PPM OXYGEN) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Turnbull, J.J., (2001) Acta Crystallogr.,Sect.D, D57, 425. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 CCD / Detector: CCD / Date: May 15, 2001 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.75→25 Å / Num. obs: 39711 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 4.1 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 335364 |
Reflection shell | *PLUS Lowest resolution: 1.82 Å / % possible obs: 99.9 % |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1GP4 Resolution: 1.75→25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1528058.88 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.2 Å2 / ksol: 0.336 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.244 |