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Yorodumi- PDB-4wqj: Crystal Structure of CYP119 from Sulfolobus acidocaldarius, Colle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wqj | ||||||
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Title | Crystal Structure of CYP119 from Sulfolobus acidocaldarius, Collected at 298K and Complexed with 4-(4-bromophenyl)-1H imidazole | ||||||
Components | Cytochrome P450 119 | ||||||
Keywords | OXIDOREDUCTASE | ||||||
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: 2.7 Å | ||||||
Authors | Madrona, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: TWO DIMENSIONAL 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 | 4wqj.cif.gz | 91 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wqj.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 4wqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/4wqj ftp://data.pdbj.org/pub/pdb/validation_reports/wq/4wqj | HTTPS FTP |
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-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 42924.027 Da / Num. of mol.: 1 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 / Production host: Escherichia coli (E. coli) References: UniProt: Q55080, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen, peroxidase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-36Y / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.85-1.2 Ammonium Sulfate 80mM Ammonium Acetate pH 4.5 20mM Ammonium Acetate pH 5.6 340mM NaCl 20% Glycerol |
-Data collection
Diffraction | Mean temperature: 298 K Ambient temp details: Collected data on fifteen crystals and merged the first 5 degrees of each one. |
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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: Apr 4, 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: 2.7→20 Å / Num. obs: 17686 / % possible obs: 97.7 % / Redundancy: 4.7 % / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.9 / % possible all: 95.5 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.7→19.945 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.08 / 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: 2.7→19.945 Å
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Refine LS restraints |
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LS refinement shell |
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