[English] 日本語
Yorodumi- PDB-8gue: Crystal Structure of narbomycin-bound cytochrome P450 PikC with t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gue | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of narbomycin-bound cytochrome P450 PikC with the unnatural amino acid p-Acetyl-L-Phenylalanine incorporated at position 238 | ||||||||||||
Components | Cytochrome P450 monooxygenase PikC | ||||||||||||
Keywords | OXIDOREDUCTASE / Narbomycin-bound / PikC / unnatural amino acid | ||||||||||||
Function / homology | Function and homology information pikromycin synthase / macrolide biosynthetic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||||||||
Biological species | Streptomyces venezuelae (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||||||||
Authors | Li, G.B. / Pan, Y.J. / Li, S.Y. / Gao, X. | ||||||||||||
Funding support | China, 3items
| ||||||||||||
Citation | Journal: Nat Commun / Year: 2023 Title: Unnatural activities and mechanistic insights of cytochrome P450 PikC gained from site-specific mutagenesis by non-canonical amino acids. Authors: Pan, Y. / Li, G. / Liu, R. / Guo, J. / Liu, Y. / Liu, M. / Zhang, X. / Chi, L. / Xu, K. / Wu, R. / Zhang, Y. / Li, Y. / Gao, X. / Li, S. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8gue.cif.gz | 219.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8gue.ent.gz | 139.5 KB | Display | PDB format |
PDBx/mmJSON format | 8gue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gue_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8gue_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8gue_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 8gue_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/8gue ftp://data.pdbj.org/pub/pdb/validation_reports/gu/8gue | HTTPS FTP |
-Related structure data
Related structure data | 2bvjS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 47219.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: unnatural amino acid p-Acetyl-L-Phenylalanine incorporated at position 238 Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: pikC, picK / Production host: Escherichia coli (E. coli) / References: UniProt: O87605, pikromycin synthase |
---|
-Non-polymers , 7 types, 321 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-TRS / | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.38 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Li2SO4, 0.1 M Bis-Tris, pH6.0, 18% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 5, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 65500 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 33.16 Å2 / CC1/2: 0.994 / Net I/σ(I): 15.75 |
Reflection shell | Resolution: 1.9→1.97 Å / Num. unique obs: 6460 / CC1/2: 0.71 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BVJ Resolution: 1.9→37.77 Å / SU ML: 0.2342 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4263 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→37.77 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|