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Yorodumi- PDB-7wzl: Crystal structure of Cytochrome P450 184A1 from streptomyces aver... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wzl | ||||||
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Title | Crystal structure of Cytochrome P450 184A1 from streptomyces avermitilis | ||||||
Components | Putative cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / Streptomyces avermitilis | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Streptomyces avermitilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Kim, V.C. / Kim, D.G. / Lee, S.G. / Lee, G.H. / Lee, S.A. / Kang, L.W. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of Cytochrome P450 184A1 from streptomyces avermitilis Authors: Kim, V.C. / Kim, D.G. / Lee, S.G. / Lee, G.H. / Lee, S.A. / Kang, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wzl.cif.gz | 102.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wzl.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 7wzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wzl_validation.pdf.gz | 810.3 KB | Display | wwPDB validaton report |
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Full document | 7wzl_full_validation.pdf.gz | 816.5 KB | Display | |
Data in XML | 7wzl_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 7wzl_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/7wzl ftp://data.pdbj.org/pub/pdb/validation_reports/wz/7wzl | HTTPS FTP |
-Related structure data
Related structure data | 6l8iS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53770.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avermitilis (bacteria) Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680 Gene: cyp21, SAVERM_5111 / Production host: Escherichia coli (E. coli) / References: UniProt: Q82D73 |
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#2: Chemical | ChemComp-HEM / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.99 % |
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Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, sitting drop Details: 15% PEG3350, 0.2 M sodium chloride, 0.1M HEPES, pH 7.0, 5% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→50 Å / Num. obs: 21998 / % possible obs: 99.2 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 56.434 |
Reflection shell | Resolution: 2.27→2.31 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 7.883 / Num. unique obs: 21998 / CC1/2: 0.937 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6L8I Resolution: 2.27→35.29 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.549 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.274 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 136.31 Å2 / Biso mean: 45.141 Å2 / Biso min: 24.53 Å2
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Refinement step | Cycle: final / Resolution: 2.27→35.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.271→2.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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