+Open data
-Basic information
Entry | Database: PDB / ID: 8e5j | |||||||||
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Title | The crystal structure of 4-n-butylbenzoic acid bound CYP199A4 | |||||||||
Components | Cytochrome P450 | |||||||||
Keywords | OXIDOREDUCTASE / P450 / Heme | |||||||||
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 HaA2 (phototrophic) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Doherty, D.Z. / Bell, S.G. / Bruning, J.B. | |||||||||
Funding support | Australia, 1items
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Citation | Journal: Chem Asian J / Year: 2022 Title: Exploring the Factors which Result in Cytochrome P450 Catalyzed Desaturation Versus Hydroxylation. Authors: Coleman, T. / Doherty, D.Z. / Zhang, T. / Podgorski, M.N. / Qiao, R. / Lee, J.H.Z. / Bruning, J.B. / De Voss, J.J. / Zhou, W. / Bell, S.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8e5j.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e5j.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 8e5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e5j_validation.pdf.gz | 1015.3 KB | Display | wwPDB validaton report |
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Full document | 8e5j_full_validation.pdf.gz | 1017.6 KB | Display | |
Data in XML | 8e5j_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 8e5j_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/8e5j ftp://data.pdbj.org/pub/pdb/validation_reports/e5/8e5j | HTTPS FTP |
-Related structure data
Related structure data | 7r8sC 7udfC 5uvbS S: Starting model for refinement C: citing same article (ref.) |
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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: 42898.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris HaA2 (phototrophic) Strain: HaA2 / Gene: RPB_3613 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2IU02 |
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#2: Chemical | ChemComp-MH0 / |
#3: Chemical | ChemComp-HX1 / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
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: 2.14 Å3/Da / Density % sol: 42.61 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion Details: 0.2 M magnesium acetate, 15-30% w/v PEG3350, 0.1 M Bis-Tris, pH 5-5.75 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→43.21 Å / Num. obs: 16355 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.29 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.254 / Rpim(I) all: 0.105 / Rrim(I) all: 0.276 / Net I/σ(I): 7.2 / Num. measured all: 109842 / Scaling rejects: 11 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UVB Resolution: 2.3→43.209 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.48 / 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 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.36 Å2 / Biso mean: 25.7239 Å2 / Biso min: 7.44 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→43.209 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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