[English] 日本語
Yorodumi- PDB-1n20: (+)-Bornyl Diphosphate Synthase: Complex with Mg and 3-aza-2,3-di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n20 | ||||||
---|---|---|---|---|---|---|---|
Title | (+)-Bornyl Diphosphate Synthase: Complex with Mg and 3-aza-2,3-dihydrogeranyl diphosphate | ||||||
Components | (+)-bornyl diphosphate synthase | ||||||
Keywords | ISOMERASE / terpene synthase fold | ||||||
Function / homology | Function and homology information (+)-camphene synthase / (+)-alpha-pinene synthase / (+)-bornyl diphosphate synthase / (+)-camphor biosynthetic process / geranyl-diphosphate cyclase activity / camphene synthase activity / diterpenoid biosynthetic process / terpene synthase activity / chloroplast / magnesium ion binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Salvia officinalis (garden sage) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Whittington, D.A. / Wise, M.L. / Urbansky, M. / Coates, R.M. / Croteau, R.B. / Christianson, D.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Bornyl Diphosphate Synthase: Structure and Strategy for Carbocation Manipulation by a Terpenoid Cyclase Authors: Whittington, D.A. / Wise, M.L. / Urbansky, M. / Coates, R.M. / Croteau, R.B. / Christianson, D.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1n20.cif.gz | 230.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1n20.ent.gz | 185.4 KB | Display | PDB format |
PDBx/mmJSON format | 1n20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/1n20 ftp://data.pdbj.org/pub/pdb/validation_reports/n2/1n20 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1n1bSC 1n1zC 1n21C 1n22C 1n23C 1n24C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer formed by the A and B chains. |
-Components
#1: Protein | Mass: 64035.664 Da / Num. of mol.: 2 / Fragment: residue 50-598 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salvia officinalis (garden sage) / Plasmid: pSBET / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) References: UniProt: O81192, (+)-bornyl diphosphate synthase #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.05 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: PEG 8000, glycerol, bis-tris, magnesium chloride, dithiothreitol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 6.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9504 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 12, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9504 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 62532 / % possible obs: 96.6 % / Redundancy: 9.2 % / Biso Wilson estimate: 31.7 Å2 / Rsym value: 0.058 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 6034 / Rsym value: 0.307 / % possible all: 94.7 |
Reflection | *PLUS Lowest resolution: 30 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1N1B Resolution: 2.3→28.77 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME, BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.7474 Å2 / ksol: 0.329226 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.7 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.32 Å / Luzzati sigma a free: 0.31 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→28.77 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.206 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|