+Open data
-Basic information
Entry | Database: PDB / ID: 5ylw | ||||||
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Title | CYP76AH1 from Salvia miltiorrhiza | ||||||
Components | Ferruginol synthase | ||||||
Keywords | OXIDOREDUCTASE / P450 / monoxygenase / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Function and homology information ferruginol synthase / diterpenoid biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / iron ion binding / heme binding / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | Salvia miltiorrhiza (Chinese salvia) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Chang, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: CYP76AH1 from Salvia miltiorrhiza Authors: Chang, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ylw.cif.gz | 224 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ylw.ent.gz | 176.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ylw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/5ylw ftp://data.pdbj.org/pub/pdb/validation_reports/yl/5ylw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55593.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salvia miltiorrhiza (Chinese salvia) / Gene: CYP76AH1 Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others) References: UniProt: S4UX02, EC: 1.14.13.190 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-MN / |
#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: 3.26 Å3/Da / Density % sol: 62.22 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / Details: HEPES, Jeffamine M-600 Reagent, manganese chloride |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 79803 / % possible obs: 99.8 % / Redundancy: 6.5 % / Net I/σ(I): 24.15 |
-Processing
Software |
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Refinement | Resolution: 1.7→48.389 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.565 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.595 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→48.389 Å
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Refine LS restraints |
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