[English] 日本語
Yorodumi- PDB-6onm: Crystal Structure of (+)-Limonene Synthase Complexed with 8,9-Dif... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6onm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of (+)-Limonene Synthase Complexed with 8,9-Difluorolinalyl Diphosphate | ||||||
Components | (+)-limonene synthase | ||||||
Keywords | LYASE / Terpene synthase / enantiomer / terpene synthase fold / monoterpene / fluoro analog / metal binding | ||||||
Function / homology | Function and homology information (R)-limonene synthase / (R)-limonene synthase activity / diterpenoid biosynthetic process / chloroplast / magnesium ion binding Similarity search - Function | ||||||
Biological species | Citrus sinensis (sweet orange) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Prem Kumar, R. / Morehouse, B.R. / Yu, Q. / Oprian, D.D. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2019 Title: Direct Evidence of an Enzyme-Generated LPP Intermediate in (+)-Limonene Synthase Using a Fluorinated GPP Substrate Analog. Authors: Morehouse, B.R. / Kumar, R.P. / Matos, J.O. / Yu, Q. / Bannister, A. / Malik, K. / Temme, J.S. / Krauss, I.J. / Oprian, D.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6onm.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6onm.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 6onm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6onm_validation.pdf.gz | 324.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6onm_full_validation.pdf.gz | 324.6 KB | Display | |
Data in XML | 6onm_validation.xml.gz | 1.3 KB | Display | |
Data in CIF | 6onm_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/6onm ftp://data.pdbj.org/pub/pdb/validation_reports/on/6onm | HTTPS FTP |
-Related structure data
Related structure data | 5uv0S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | (+)- Mass: 70441.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrus sinensis (sweet orange) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Variant (production host): BL21-CodonPlus(DE3) / References: UniProt: A0A1C9J6A7, (R)-limonene synthase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-MWG / ( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.74 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 16% PEG8000, 100 mM Tris pH 7.5, 350 mM sodium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 20, 2017 / Details: Mirrors |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 23172 / % possible obs: 99.8 % / Redundancy: 26.7 % / Biso Wilson estimate: 70.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 27.8 % / Rmerge(I) obs: 1.77 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3302 / CC1/2: 0.822 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5uv0 Resolution: 2.7→19.957 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.81
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.04 Å2 / Biso mean: 71.4766 Å2 / Biso min: 38.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→19.957 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
|