+Open data
-Basic information
Entry | Database: PDB / ID: 6lcc | ||||||
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Title | Crystal structure of AaTPS apo | ||||||
Components | AaTPS | ||||||
Keywords | LYASE / terpene cyclase / terpene synthase | ||||||
Biological species | Alternaria alternata (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | He, H. / Mori, T. / Abe, I. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Crystal structure of AaTPS Authors: He, H. / Mori, T. / Abe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lcc.cif.gz | 161 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lcc.ent.gz | 125.3 KB | Display | PDB format |
PDBx/mmJSON format | 6lcc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/6lcc ftp://data.pdbj.org/pub/pdb/validation_reports/lc/6lcc | HTTPS FTP |
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-Related structure data
Related structure data | 6lcdC 2oa6S 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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-Components
#1: Protein | Mass: 48238.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alternaria alternata (fungus) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #2: 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: 3.14 Å3/Da / Density % sol: 60.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, Ammonium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→46.796 Å / Num. obs: 38215 / % possible obs: 100 % / Redundancy: 5.7 % / Biso Wilson estimate: 48.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.6→2.72 Å / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4595 / CC1/2: 0.818 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OA6 Resolution: 2.6→46.796 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.87 Å2 / Biso mean: 48.4217 Å2 / Biso min: 20.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→46.796 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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