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Yorodumi- PDB-4b0n: Crystal structure of PKS-I from the brown algae Ectocarpus siliculosus -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b0n | ||||||
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Title | Crystal structure of PKS-I from the brown algae Ectocarpus siliculosus | ||||||
Components | POLYKETIDE SYNTHASE III | ||||||
Keywords | TRANSFERASE / POLYPHENOL BIOSYNTHESIS / ARACHIDONYL GROUP | ||||||
Function / homology | Function and homology information biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups Similarity search - Function | ||||||
Biological species | ECTOCARPUS SILICULOSUS (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Leroux, C. / Meslet-Cladiere, L. / Delage, L. / Goulitquer, S. / Leblanc, C. / Ar Gall, E. / Stiger-Pouvreau, V. / Potin, P. / Czjzek, M. | ||||||
Citation | Journal: Plant Cell / Year: 2013 Title: Structure/Function Analysis of a Type III Polyketide Synthase in the Brown Alga Ectocarpus Siliculosus Reveals a Biochemical Pathway in Phlorotannin Monomer Biosynthesis. Authors: Meslet-Cladiere, L. / Delage, L. / J-J Leroux, C. / Goulitquer, S. / Leblanc, C. / Creis, E. / Gall, E.A. / Stiger-Pouvreau, V. / Czjzek, M. / Potin, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b0n.cif.gz | 297.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b0n.ent.gz | 242.8 KB | Display | PDB format |
PDBx/mmJSON format | 4b0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b0n_validation.pdf.gz | 785.5 KB | Display | wwPDB validaton report |
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Full document | 4b0n_full_validation.pdf.gz | 797.3 KB | Display | |
Data in XML | 4b0n_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 4b0n_validation.cif.gz | 45.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/4b0n ftp://data.pdbj.org/pub/pdb/validation_reports/b0/4b0n | HTTPS FTP |
-Related structure data
Related structure data | 1tedS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.818, 0.4, 0.413), Vector: |
-Components
#1: Protein | Mass: 44509.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COVALENT LINK BETWEEN C 194 AND THE ACETYL GROUP OF THE FATTY ACID LIGAND Source: (gene. exp.) ECTOCARPUS SILICULOSUS (eukaryote) / Strain: EC32 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS-RILP References: UniProt: D8LJ35, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | ARACHIDONI | |
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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: 2.39 Å3/Da / Density % sol: 48.5 % / Description: NONE |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 3 MICROLITER DROPS OF PROTEIN AT 7 MG/ML WERE MIXED WITH 1.5 MICROLITERS OF CRYSTALLIZATION BUFFER (0.1 M BICINE PH 8, 18% PEG 6000) USING THE HANGING DROP VAPOR DIFFUSION METHOD AT 19 DEGREES CELSIUS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 |
Detector | Type: ADSC QUANTUM Q4 / Detector: CCD / Date: Feb 23, 2011 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→49 Å / Num. obs: 18963 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.85→3.02 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.4 / % possible all: 77.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TED Resolution: 2.85→49.4 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.897 / SU B: 24.507 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. DISORDERED RESIDUES AND LIGAND WERE MODELED WITH OCCUPANCY LOWER THAN 1.00.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.972 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→49.4 Å
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Refine LS restraints |
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