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Open data
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Basic information
Entry | Database: PDB / ID: 8euk | ||||||
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Title | cytochrome P450terp (cyp108A1) bound to ethylene glycol | ||||||
![]() | Cytochrome P450-terp | ||||||
![]() | OXIDOREDUCTASE / monooxygenase / complex / substrate / heme | ||||||
Function / homology | ![]() Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gable, J.A. / Follmer, A.H. / Poulos, T.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cooperative Substrate Binding Controls Catalysis in Bacterial Cytochrome P450terp (CYP108A1). Authors: Gable, J.A. / Poulos, T.L. / Follmer, A.H. | ||||||
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 | ![]() | 149.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 853.7 KB | Display | ![]() |
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Full document | ![]() | 855.4 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8euhC ![]() 8eulC ![]() 1cptS S: Starting model for refinement C: citing same article ( |
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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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 50148.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P33006, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.06 M magnesium chloride hexahyrate, 0.06 M calcium chloride dihydrate, 0.1 M sodium HEPES and MOPS (acid) pH 7.5, 20% v/v ethylene glycol, 10% v/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→59.52 Å / Num. obs: 46098 / % possible obs: 99.92 % / Redundancy: 20.1 % / Biso Wilson estimate: 27.62 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.01765 / Net I/σ(I): 27.93 |
Reflection shell | Resolution: 1.984→2.055 Å / Mean I/σ(I) obs: 11.55 / Num. unique obs: 4465 / CC1/2: 0.995 / Rpim(I) all: 0.04957 / % possible all: 99.98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CPT Resolution: 1.98→59.52 Å / SU ML: 0.154 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.8695 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 35.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→59.52 Å
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Refine LS restraints |
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LS refinement shell |
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