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Open data
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Basic information
Entry | Database: PDB / ID: 5l1p | ||||||
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Title | X-ray Structure of Cytochrome P450 PntM with Pentalenolactone | ||||||
![]() | Pentalenolactone synthase | ||||||
![]() | OXIDOREDUCTASE / PntM / cytochrome P450 / pentalenolactone | ||||||
Function / homology | ![]() pentalenolactone synthase / pentalenolactone biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor / cholest-4-en-3-one 26-monooxygenase activity / antibiotic biosynthetic process / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Duan, L. / Jogl, G. / Cane, D.E. | ||||||
![]() | ![]() Title: The Cytochrome P450-Catalyzed Oxidative Rearrangement in the Final Step of Pentalenolactone Biosynthesis: Substrate Structure Determines Mechanism. Authors: Duan, L. / Jogl, G. / Cane, D.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.9 KB | Display | ![]() |
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PDB format | ![]() | 144.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5l1oC ![]() 5l1qC ![]() 5l1rC ![]() 5l1sC ![]() 5l1tC ![]() 5l1uC ![]() 5l1vC ![]() 5l1wC ![]() 2x9pS C: citing same article ( S: Starting model for refinement |
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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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 44504.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-7PT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.26 % / Mosaicity: 0.22 ° |
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Crystal grow | Temperature: 288 K / Method: evaporation / pH: 9 / Details: Bicine, sodium citrate, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 31, 2014 / Details: mirrors | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.28→45.33 Å / Num. obs: 27950 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 20.85 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.303 / Net I/σ(I): 6.4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2x9p Resolution: 2.28→45.326 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.38 Å2 / Biso mean: 27.1348 Å2 / Biso min: 9.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.28→45.326 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 20.8177 Å / Origin y: 26.8278 Å / Origin z: 20.2422 Å
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Refinement TLS group |
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