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Yorodumi- PDB-1gp4: Anthocyanidin synthase from Arabidopsis thaliana (selenomethionin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gp4 | ||||||
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Title | Anthocyanidin synthase from Arabidopsis thaliana (selenomethionine substituted) | ||||||
Components | ANTHOCYANIDIN SYNTHASE | ||||||
Keywords | OXIDOREDUCTASE / OXYGENASE / 2-OXOGLUTARATE DEPENDENT DIOXYGENASE / FLAVONOID BIOSYNTHESIS | ||||||
Function / homology | Function and homology information anthocyanidin synthase / proanthocyanidin biosynthetic process / leucocyanidin oxygenase activity / anthocyanin-containing compound biosynthetic process / response to jasmonic acid / vacuole organization / L-ascorbic acid binding / response to wounding / metal ion binding Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Wilmouth, R.C. / Turnbull, J.J. / Welford, R.W.D. / Clifton, I.J. / Prescott, A.G. / Schofield, C.J. | ||||||
Citation | Journal: Structure / Year: 2002 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: Journal: Chem.Commun. / Year: 2000 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gp4.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gp4.ent.gz | 67.3 KB | Display | PDB format |
PDBx/mmJSON format | 1gp4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gp4_validation.pdf.gz | 455 KB | Display | wwPDB validaton report |
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Full document | 1gp4_full_validation.pdf.gz | 459.3 KB | Display | |
Data in XML | 1gp4_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 1gp4_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/1gp4 ftp://data.pdbj.org/pub/pdb/validation_reports/gp/1gp4 | HTTPS FTP |
-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: 40779.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET-24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96323, EC: 1.14.11.19 |
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#2: Chemical | ChemComp-AKG / |
#3: Chemical | ChemComp-MES / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 30% (W/V) PEG 2000 MONOMETHYLETHER, 50 MM MES, 100 MM SODIUM CITRATE, 200 MM AMMONIUM ACETATE, 5 MM IRON(II) SULPHATE, 10 MM POTASSIUM ALPHA-KETOGLUTARATE, 10 MM SODIUM ASCORBATE, PH 6.5, ...Details: 30% (W/V) PEG 2000 MONOMETHYLETHER, 50 MM MES, 100 MM SODIUM CITRATE, 200 MM AMMONIUM ACETATE, 5 MM IRON(II) SULPHATE, 10 MM POTASSIUM ALPHA-KETOGLUTARATE, 10 MM SODIUM ASCORBATE, 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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.91841,0.97855,0.97885 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 2000 / Details: MIRRORS | ||||||||||||
Radiation | Monochromator: SI / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→36.5 Å / Num. obs: 23462 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 9.8 | ||||||||||||
Reflection shell | Resolution: 2.1→2.21 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.8 / % possible all: 100 | ||||||||||||
Reflection | *PLUS Num. measured all: 348658 | ||||||||||||
Reflection shell | *PLUS Highest resolution: 2.1 Å / % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1571181.72 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.5 Å2 / ksol: 0.336 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / 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: 0.192 |