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Open data
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Basic information
Entry | Database: PDB / ID: 1n1b | ||||||
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Title | Crystal Structure of (+)-Bornyl Diphosphate Synthase from Sage | ||||||
![]() | (+)-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 | ![]() | 233.2 KB | Display | ![]() |
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PDB format | ![]() | 186.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.8 KB | Display | ![]() |
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Full document | ![]() | 456 KB | Display | |
Data in XML | ![]() | 43.1 KB | Display | |
Data in CIF | ![]() | 62.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1n1zC ![]() 1n20C ![]() 1n21C ![]() 1n22C ![]() 1n23C ![]() 1n24C 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 the dimer contained in the asymmetric unit. |
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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 | #3: Chemical | ChemComp-HG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.68 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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, potassium mercury thiocyanate, 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: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 12, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 97291 / % possible obs: 99.8 % / Redundancy: 11.6 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.051 / Net I/σ(I): 33.9 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 4 / Num. unique all: 4640 / Rsym value: 0.442 / % possible all: 97.1 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 633848 / Rmerge(I) obs: 0.051 |
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Processing
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Refinement | Method to determine structure: ![]() Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.1991 Å2 / ksol: 0.359857 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.9 Å2
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Refine analyze | Luzzati coordinate error free: 0.27 Å / Luzzati sigma a free: 0.2 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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