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- PDB-4ego: The X-ray crystal structure of CYP199A4 in complex with indole-6-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ego | ||||||
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Title | The X-ray crystal structure of CYP199A4 in complex with indole-6-carboxylic acid | ||||||
![]() | Cytochrome P450 | ||||||
![]() | OXIDOREDUCTASE / Cytochrome P450 / Secondary metabolites biosynthesis / transport / catabolism | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Zhou, W. / Bell, S.G. / Yang, W. / Zhou, R.M. / Tan, A.B.H. / Wong, L.-L. | ||||||
![]() | ![]() Title: Investigation of the substrate range of CYP199A4: modification of the partition between hydroxylation and desaturation activities by substrate and protein engineering Authors: Bell, S.G. / Zhou, R.M. / Yang, W. / Tan, A.B.H. / Gentleman, A.S. / Wong, L.-L. / Zhou, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 343.9 KB | Display | ![]() |
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PDB format | ![]() | 277.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 75.6 KB | Display | |
Data in CIF | ![]() | 107.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4egmC ![]() 4egnC ![]() 4egpC ![]() 4dnzS 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 44587.430 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: HaA2 / Gene: RPB_3613 / Plasmid: pET28a / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 1250 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/1F1.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1F1.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-1F1 / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.72 Å3/Da / Density % sol: 66.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M Bis-tris, 1.45M (NH4)2SO4, 0.1M NaCl, 1.0M Sodium iodide, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. all: 261176 / Num. obs: 235058 / % possible obs: 90 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.055 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.76→1.82 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 2.4 / Num. unique all: 17213 / Rsym value: 0.371 / % possible all: 66.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DNZ Resolution: 1.76→39 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.997 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.762→1.808 Å / Rfactor Rfree error: 0.098 / Total num. of bins used: 20
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