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Yorodumi- PDB-1u0w: An Aldol Switch Discovered in Stilbene Synthases Mediates Cycliza... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u0w | ||||||
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Title | An Aldol Switch Discovered in Stilbene Synthases Mediates Cyclization Specificity of Type III Polyketide Synthases: 18xCHS+resveratrol Structure | ||||||
Components | Chalcone synthase 2 | ||||||
Keywords | TRANSFERASE / type III polyketide synthase / PKS / condensing enzyme / thiolase fold / alpha-beta-alpha-beta-alpha fold / aldol switch / catalytic triad / engineered resveratrol synthase / RS / STS / CHS / chalcone synthase / stilbene synthase | ||||||
Function / homology | Function and homology information chalcone biosynthetic process / : / chalcone synthase / naringenin-chalcone synthase activity / flavonoid biosynthetic process / polyketide biosynthetic process Similarity search - Function | ||||||
Biological species | Medicago sativa (alfalfa) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Austin, M.B. / Bowman, M.E. / Ferrer, J.-L. / Schroder, J. / Noel, J.P. | ||||||
Citation | Journal: Chem.Biol. / Year: 2004 Title: An Aldol Switch Discovered in Stilbene Synthases Mediates Cyclization Specificity of Type III Polyketide Synthases Authors: Austin, M.B. / Bowman, M.E. / Ferrer, J.-L. / Schroder, J. / Noel, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u0w.cif.gz | 327.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u0w.ent.gz | 265.8 KB | Display | PDB format |
PDBx/mmJSON format | 1u0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u0w_validation.pdf.gz | 481.6 KB | Display | wwPDB validaton report |
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Full document | 1u0w_full_validation.pdf.gz | 517.5 KB | Display | |
Data in XML | 1u0w_validation.xml.gz | 71.7 KB | Display | |
Data in CIF | 1u0w_validation.cif.gz | 103 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/1u0w ftp://data.pdbj.org/pub/pdb/validation_reports/u0/1u0w | HTTPS FTP |
-Related structure data
Related structure data | 1u0uC 1u0vSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a homodimer: represented here by Chains A:B and C:D (two independent homodimers) |
-Components
#1: Protein | Mass: 42874.324 Da / Num. of mol.: 4 Mutation: D96A, V98L, V99A, V100M, T131S, S133T, G134T, V135P, M137L, Y157V, M158G, M159V, Y160F, Q161H, L268K, K269G, D270A, G273D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago sativa (alfalfa) / Gene: CHS2 / Plasmid: pHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30074, chalcone synthase #2: Chemical | ChemComp-STL / #3: 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: 2.19 Å3/Da / Density % sol: 43.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, ammonium acetate, HEPES-Na+ buffer, ethylene glycol, resveratrol, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.773 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 9, 2001 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.773 Å / Relative weight: 1 |
Reflection | Resolution: 2→49.34 Å / Num. all: 93036 / Num. obs: 93036 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.4 Å2 |
Reflection shell | Resolution: 2→2.13 Å / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U0V Resolution: 2→49.34 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1753601.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.0965 Å2 / ksol: 0.343586 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→49.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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