+Open data
-Basic information
Entry | Database: PDB / ID: 3wd7 | ||||||
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Title | Type III polyketide synthase | ||||||
Components | Type III polyketide synthases acridone synthase | ||||||
Keywords | TRANSFERASE / acridone synthase / Type III polyketide synthase / acyltransferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Citrus microcarpa (calamondin) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Mori, T. / Shimokawa, Y. / Matsui, T. / Kato, R. / Sugio, S. / 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 | 3wd7.cif.gz | 175.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wd7.ent.gz | 137.3 KB | Display | PDB format |
PDBx/mmJSON format | 3wd7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wd7_validation.pdf.gz | 903.1 KB | Display | wwPDB validaton report |
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Full document | 3wd7_full_validation.pdf.gz | 909.5 KB | Display | |
Data in XML | 3wd7_validation.xml.gz | 32.8 KB | Display | |
Data in CIF | 3wd7_validation.cif.gz | 46.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/3wd7 ftp://data.pdbj.org/pub/pdb/validation_reports/wd/3wd7 | HTTPS FTP |
-Related structure data
Related structure data | 3wd8C 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44285.879 Da / Num. of mol.: 2 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: U3KRF0*PLUS, acridone synthase #2: Chemical | #3: Chemical | ChemComp-NI / #4: Chemical | #5: 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: 3.17 Å3/Da / Density % sol: 61.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM HEPES-NaOH, 1400mM ammonium sulfate, 2mM NiCl2, 2mM CoA SH, pH 7.5, 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: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 9, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 49243 / Num. obs: 48865 / % possible obs: 99.57 % |
Reflection shell | Resolution: 2.35→2.39 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CGK Resolution: 2.35→34.524 Å / Occupancy max: 1 / Occupancy min: 0.94 / FOM work R set: 0.8538 / SU ML: 0.22 / σ(F): 0.61 / Phase error: 20.65 / 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: 90.76 Å2 / Biso mean: 33.6445 Å2 / Biso min: 16.87 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→34.524 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: 17
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