[English] 日本語
Yorodumi- PDB-3awk: Crystal structure of the polyketide synthase 1 from huperzia serrata -
+Open data
-Basic information
Entry | Database: PDB / ID: 3awk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the polyketide synthase 1 from huperzia serrata | ||||||
Components | Chalcone synthase-like polyketide synthase | ||||||
Keywords | TRANSFERASE / type III polyketide synthase / chalcone synthase | ||||||
Function / homology | Function and homology information polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Huperzia serrata (toothed club-moss) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Morita, H. / Kondo, S. / Kato, R. / Sugio, S. / Kohno, T. / Abe, I. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Synthesis of unnatural alkaloid scaffolds by exploiting plant polyketide synthase. Authors: Morita, H. / Yamashita, M. / Shi, S.P. / Wakimoto, T. / Kondo, S. / Kato, R. / Sugio, S. / Kohno, T. / Abe, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3awk.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3awk.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 3awk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3awk_validation.pdf.gz | 453.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3awk_full_validation.pdf.gz | 455 KB | Display | |
Data in XML | 3awk_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 3awk_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/3awk ftp://data.pdbj.org/pub/pdb/validation_reports/aw/3awk | HTTPS FTP |
-Related structure data
Related structure data | 3awjC 1cgkS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 43662.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Huperzia serrata (toothed club-moss) / Gene: Pks1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: A3E7Z7 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.92 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES-NaOH, 1925mM ammonium sulfate, 1,1,1,3,3,3-hexafluoro-2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.82656 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 15, 2006 |
Radiation | Monochromator: bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82656 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 27623 / Num. obs: 27623 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.056 / Net I/σ(I): 49.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 10.8 / Num. unique all: 2862 / Rsym value: 0.284 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CGK Resolution: 2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
| ||||||||||||||||||||
Refine LS restraints |
|