+Open data
-Basic information
Entry | Database: PDB / ID: 3wd8 | ||||||
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Title | TypeIII polyketide synthases | ||||||
Components | Type III polyketide synthase quinolone synthase | ||||||
Keywords | TRANSFERASE / quinolone synthase / Type III polyketide synthase / Acyltransferase | ||||||
Function / homology | Function and homology information polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Citrus microcarpa (calamondin) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.463 Å | ||||||
Authors | Mori, T. / Shimokawa, Y. / Matsui, T. / Morita, H. / Abe, I. | ||||||
Citation | Journal: To be Published Title: Cloning, characterization, and crystal structure analysis of novel type III polyketide synthases from Citrus microcarpa Authors: Mori, T. / Shimokawa, Y. / Matsui, T. / Kinjo, K. / Kato, R. / Noguchi, H. / Sugio, S. / Morita, H. / Abe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wd8.cif.gz | 302.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wd8.ent.gz | 246.4 KB | Display | PDB format |
PDBx/mmJSON format | 3wd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wd8_validation.pdf.gz | 460.3 KB | Display | wwPDB validaton report |
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Full document | 3wd8_full_validation.pdf.gz | 477.2 KB | Display | |
Data in XML | 3wd8_validation.xml.gz | 54.8 KB | Display | |
Data in CIF | 3wd8_validation.cif.gz | 75.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/3wd8 ftp://data.pdbj.org/pub/pdb/validation_reports/wd/3wd8 | HTTPS FTP |
-Related structure data
Related structure data | 3wd7C 1cgkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44489.215 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrus microcarpa (calamondin) / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: U3KRF1*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN THE UNIPROT DATABASE. ...THE SEQUENCE DATABASE REFERENCES | |
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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: 2.13 Å3/Da / Density % sol: 42.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 50mM Tris-HCl, 18% PEG3350, 4%(v/v) 1-propanol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.463→19.987 Å / Num. all: 52974 / Num. obs: 52852 / % possible obs: 99.4 % / Biso Wilson estimate: 43.44 Å2 |
Reflection shell | Resolution: 2.47→2.51 Å / Redundancy: 3.85 % / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CGK Resolution: 2.463→19.987 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7927 / SU ML: 0.38 / σ(F): 1.35 / Phase error: 27.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.42 Å2 / Biso mean: 39.0751 Å2 / Biso min: 13.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.463→19.987 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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