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Yorodumi- PDB-4wpd: X-ray Crystal Structure of CYP119 complexed with 4-(4-flouropheny... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wpd | ||||||
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Title | X-ray Crystal Structure of CYP119 complexed with 4-(4-flourophenyl)-1H-imidazole | ||||||
Components | Cytochrome P450 119 | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / 4-(4-flourophenyl)-1H-imidazole ligand bound | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / lactoperoxidase activity / peroxidase / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.001 Å | ||||||
Authors | Madrona, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: TWO DIMENTIONAL NMR AND X-RAY ANALYSIS OF CYP119 LIGAND DEPENDENT CONFORMATIONAL DYNAMICS Authors: Basudhar, D. / Madrona, Y. / Kandel, S. / Lampe, J.N. / Ortiz de Montellano, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wpd.cif.gz | 183.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wpd.ent.gz | 143.4 KB | Display | PDB format |
PDBx/mmJSON format | 4wpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wpd_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4wpd_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4wpd_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 4wpd_validation.cif.gz | 54.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/4wpd ftp://data.pdbj.org/pub/pdb/validation_reports/wp/4wpd | HTTPS FTP |
-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 42924.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic) Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 Gene: cyp119, Saci_2081 / Plasmid: PcWori / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 alpha References: UniProt: Q55080, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen, peroxidase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: Well solution contained: 2% PEG 8K, 400 mM MgCl2 and 100 mM LiCl2 Additive contained: 1.4 ammonium sulfate, 80 mM sodium acetate, pH 4.5, 20 mM sodium acetate pH 5.6, 20% glycerol, and 200 mM NaCl PH range: 4.5-5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.1 Å / Num. obs: 54418 / % possible obs: 99.1 % / Redundancy: 3.7 % / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 4 / % possible all: 96.6 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.001→36.42 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 18.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.001→36.42 Å
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Refine LS restraints |
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LS refinement shell |
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