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Yorodumi- PDB-5yqa: The crystal structure of CYP199A4 binding with 4-n-Propyl benzoic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yqa | ||||||
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Title | The crystal structure of CYP199A4 binding with 4-n-Propyl benzoic acid | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / metabolites biosynthesis / catabolism Cytoplasm | ||||||
Function / homology | Function and homology information cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | ||||||
Authors | Zhou, W. / Zhang, T. / Qiao, R. / Bell, S. / Coleman, T. | ||||||
Citation | Journal: To Be Published Title: The crystal structure of CYP199A4 binding with 4-n-Propyl benzoic acid Authors: Coleman, T. / Zhang, T. / Qiao, R. / Zhou, W. / Beii, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yqa.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yqa.ent.gz | 75.7 KB | Display | PDB format |
PDBx/mmJSON format | 5yqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yqa_validation.pdf.gz | 827.7 KB | Display | wwPDB validaton report |
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Full document | 5yqa_full_validation.pdf.gz | 830.9 KB | Display | |
Data in XML | 5yqa_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 5yqa_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/5yqa ftp://data.pdbj.org/pub/pdb/validation_reports/yq/5yqa | HTTPS FTP |
-Related structure data
Related structure data | 5yqhC 4dnzS S: Starting model for refinement C: citing same article (ref.) |
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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: 44587.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (strain HaA2) (phototrophic) Strain: HaA2 / Gene: RPB_3613 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2IU02 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-8ZU / |
#4: Chemical | ChemComp-CL / |
#5: 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: 2.01 Å3/Da / Density % sol: 38.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.25M NaCl, 1.5M (NH4)2SO4, 0.1M Bis-Tris, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→50 Å / Num. obs: 72080 / % possible obs: 98.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.6 |
Reflection shell | Resolution: 1.38→1.4 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DNZ Resolution: 1.38→33.345 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.96
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Bsol: 42.379 Å2 / ksol: 0.357 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.38→33.345 Å
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Refine LS restraints |
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LS refinement shell |
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