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- PDB-7jxb: The crystal structure of 4-(3'-methoxyphenyl)benzoic acid-bound C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7jxb | ||||||
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Title | The crystal structure of 4-(3'-methoxyphenyl)benzoic acid-bound CYP199A4 | ||||||
![]() | Cytochrome P450 | ||||||
![]() | OXIDOREDUCTASE / Cytochrome / P450 / Monooxygenase / Heme / Oxygen Insertion | ||||||
Function / homology | ![]() cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Doherty, D.Z. / Bell, S.G. / Bruning, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Enabling Aromatic Hydroxylation in a Cytochrome P450 Monooxygenase Enzyme through Protein Engineering. Authors: Coleman, T. / Lee, J.Z.H. / Kirk, A.M. / Doherty, D.Z. / Podgorski, M.N. / Pinidiya, D.K. / Bruning, J.B. / De Voss, J.J. / Krenske, E.H. / Bell, S.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.8 KB | Display | ![]() |
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PDB format | ![]() | 76 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 32.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tndC ![]() 7tnfC ![]() 7tnuC ![]() 8d39C ![]() 5uvbS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() Strain: HaA2 / Gene: RPB_3613 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-VLG / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.51 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop Details: 0.2 M magnesium acetate, 100 mM Bis-Tris (adjusted with acetic acid to pH 5.0-5.75), 20-32% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 27, 2018 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.655→43.14 Å / Num. obs: 39399 / % possible obs: 99.6 % / Redundancy: 7.4 % / Biso Wilson estimate: 8.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.022 / Rrim(I) all: 0.06 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.66→1.68 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.186 / Num. unique obs: 1875 / CC1/2: 0.983 / Rpim(I) all: 0.077 / Rrim(I) all: 0.201 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5UVB Resolution: 1.655→43.136 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.37 / 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: 66.36 Å2 / Biso mean: 10.8247 Å2 / Biso min: 1.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.655→43.136 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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