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- PDB-1n23: (+)-Bornyl diphosphate synthase: Complex with Mg, pyrophosphate, ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1n23 | ||||||
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Title | (+)-Bornyl diphosphate synthase: Complex with Mg, pyrophosphate, and (1R,4S)-2-azabornane | ||||||
![]() | (+)-bornyl diphosphate synthase | ||||||
![]() | ISOMERASE / terpene synthase fold | ||||||
Function / homology | ![]() (+)-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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Whittington, D.A. / Wise, M.L. / Urbansky, M. / Coates, R.M. / Croteau, R.B. / Christianson, D.W. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 230 KB | Display | ![]() |
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PDB format | ![]() | 184.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.7 KB | Display | ![]() |
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Full document | ![]() | 486.2 KB | Display | |
Data in XML | ![]() | 40.6 KB | Display | |
Data in CIF | ![]() | 56.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1n1bSC ![]() 1n1zC ![]() 1n20C ![]() 1n21C ![]() 1n22C ![]() 1n24C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a dimer formed by chains A and B. |
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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.) ![]() ![]() ![]() References: UniProt: O81192, (+)-bornyl diphosphate synthase #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.4 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 56932 / % possible obs: 99.5 % / Redundancy: 8.3 % / Biso Wilson estimate: 36.2 Å2 / Rsym value: 0.048 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 5555 / Rsym value: 0.294 / % possible all: 98.9 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 30 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1N1B Resolution: 2.4→29.36 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.3419 Å2 / ksol: 0.329098 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.3 Å2
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Refine analyze | Luzzati coordinate error free: 0.34 Å / Luzzati sigma a free: 0.31 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.4 Å / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.208 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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