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- PDB-6wkd: Crystal structure of pentalenene synthase complexed with 12,13-di... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wkd | ||||||
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Title | Crystal structure of pentalenene synthase complexed with 12,13-difluorofarnesyl diphosphate | ||||||
![]() | Pentalenene synthase | ||||||
![]() | METAL BINDING PROTEIN / LYASE/INHIBITOR / Terpene synthase / terpene synthase fold / sesquiterpene / fluoro analog / metal binding / LYASE-INHIBITOR complex | ||||||
Function / homology | ![]() pentalenene synthase / pentalenene synthase activity / antibiotic biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Prem Kumar, R. / Matos, J.O. / Oprian, D.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism Underlying Anti-Markovnikov Addition in the Reaction of Pentalenene Synthase. Authors: Matos, J.O. / Kumar, R.P. / Ma, A.C. / Patterson, M. / Krauss, I.J. / Oprian, D.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.8 KB | Display | ![]() |
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PDB format | ![]() | 105.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6wkcC ![]() 6wkeC ![]() 6wkfC ![]() 6wkgC ![]() 6wkhC ![]() 6wkiC ![]() 6wkjC ![]() 1ps1S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38050.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FDF / ( | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.35 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 0.8-1.2 M sodium tartrate, 100 mM Tris, and 5 mM DTT PH range: 7.5 - 9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2018 / Details: Mirrors |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 54634 / % possible obs: 99.9 % / Redundancy: 20.4 % / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 21 % / Rmerge(I) obs: 1.72 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7917 / CC1/2: 0.75 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PS1 Resolution: 2.2→19.971 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.1 Å2 / Biso mean: 48.2834 Å2 / Biso min: 25.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→19.971 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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