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- PDB-8hge: Crystal structure of the CYP153A mutant V456A from Marinobacter a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hge | ||||||
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Title | Crystal structure of the CYP153A mutant V456A from Marinobacter aquaeolei in complex with 12-hydroxydodecanoic acid | ||||||
![]() | Cytochrome P450 | ||||||
![]() | OXIDOREDUCTASE / CYP153A / Complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Jiang, Y. / Cong, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the CYP153A mutant V456A from Marinobacter aquaeolei in complex with 12-hydroxydodecanoic acid Authors: Jiang, Y. / Cong, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197.9 KB | Display | ![]() |
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PDB format | ![]() | 150.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 939.3 KB | Display | ![]() |
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Full document | ![]() | 940.6 KB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fygS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 55250.988 Da / Num. of mol.: 1 / Mutation: V456A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-12H / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M Li2SO4, 0.1 M HEPES 7.0, 26% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. obs: 63827 / % possible obs: 95.6 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.031 / Rrim(I) all: 0.057 / Χ2: 0.894 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.53→1.56 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.132 / Num. unique obs: 2949 / CC1/2: 0.964 / Rpim(I) all: 0.097 / Rrim(I) all: 0.165 / Χ2: 0.794 / % possible all: 87.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5FYG Resolution: 1.53→31.54 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 17.28 / 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: 1.53→31.54 Å
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Refine LS restraints |
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LS refinement shell |
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