+Open data
-Basic information
Entry | Database: PDB / ID: 5l1p | ||||||
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Title | X-ray Structure of Cytochrome P450 PntM with Pentalenolactone | ||||||
Components | Pentalenolactone synthase | ||||||
Keywords | OXIDOREDUCTASE / PntM / cytochrome P450 / pentalenolactone | ||||||
Function / homology | Function and homology information 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 | Streptomyces arenae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Duan, L. / Jogl, G. / Cane, D.E. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l1p.cif.gz | 184.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l1p.ent.gz | 144.5 KB | Display | PDB format |
PDBx/mmJSON format | 5l1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l1p_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5l1p_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5l1p_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 5l1p_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/5l1p ftp://data.pdbj.org/pub/pdb/validation_reports/l1/5l1p | HTTPS FTP |
-Related structure data
Related structure data | 5l1oC 5l1qC 5l1rC 5l1sC 5l1tC 5l1uC 5l1vC 5l1wC 2x9pS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Streptomyces arenae (bacteria) / Strain: Tu469 / Gene: pntM / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E3VWI3, pentalenolactone synthase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-7PT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54179 Å | ||||||||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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