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- PDB-5gul: Crystal structure of Tris/PPix2/Mg2+ bound form of cyclolavanduly... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gul | ||||||
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Title | Crystal structure of Tris/PPix2/Mg2+ bound form of cyclolavandulyl diphosphate synthase (CLDS) from Streptomyces sp. CL190 | ||||||
![]() | Cyclolavandulyl diphosphate synthase | ||||||
![]() | BIOSYNTHETIC PROTEIN / cyclolavandulyl diphosphate synthase / cis-prenyltransferase / Streptomyces sp. CL190 / Tris / PPi / Mg2+ | ||||||
Function / homology | ![]() plastid membrane organization / dehydrodolichyl diphosphate synthase activity / Z-farnesyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / response to cold / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tomita, T. / Kobayashi, M. / Nishiyama, M. / Kuzuyama, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and Mechanism of the Monoterpene Cyclolavandulyl Diphosphate Synthase that Catalyzes Consecutive Condensation and Cyclization. Authors: Tomita, T. / Kobayashi, M. / Karita, Y. / Yasuno, Y. / Shinada, T. / Nishiyama, M. / Kuzuyama, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190.5 KB | Display | ![]() |
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PDB format | ![]() | 150 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 501.1 KB | Display | ![]() |
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Full document | ![]() | 514.4 KB | Display | |
Data in XML | ![]() | 35.4 KB | Display | |
Data in CIF | ![]() | 49.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gukSC 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26676.123 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: CL190 / Production host: ![]() ![]() #2: Chemical | ChemComp-POP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-TRS / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100mM HEPES NaOH pH 7.0, 24% PEG 2000 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→55.04 Å / Num. obs: 92115 / % possible obs: 85.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.73→1.76 Å / Rmerge(I) obs: 0.434 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5GUK Resolution: 1.73→55.04 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.615 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.159 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.102 Å2
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Refinement step | Cycle: 1 / Resolution: 1.73→55.04 Å
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Refine LS restraints |
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