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- PDB-4apy: Ethylene glycol-bound form of P450 CYP125A3 from Mycobacterium sm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4apy | ||||||
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Title | Ethylene glycol-bound form of P450 CYP125A3 from Mycobacterium smegmatis | ||||||
![]() | P450 HEME-THIOLATE PROTEIN | ||||||
![]() | OXIDOREDUCTASE / CHOLESTEROL METABOLISM | ||||||
Function / homology | ![]() cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / cholest-4-en-3-one 26-monooxygenase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Frank, D.J. / Garcia Fernandez, E. / Kells, P.M. / Garcia Lopez, J.L. / Podust, L.M. / Ortiz de Montellano, P.R. | ||||||
![]() | ![]() Title: A Highly Conserved Mycobacterial Cholesterol Catabolic Pathway. Authors: Garcia-Fernandez, E. / Frank, D.J. / Galan, B. / Kells, P.M. / Podust, L.M. / Garcia, J.L. / Ortiz de Montellano, P.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.6 KB | Display | ![]() |
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PDB format | ![]() | 80.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 827.7 KB | Display | ![]() |
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Full document | ![]() | 834.3 KB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 32.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yooC ![]() 3zbyC ![]() 2x5wS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 47986.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PCW / Production host: ![]() ![]() | ||||||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Nonpolymer details | 1,2-ETHANEDIOL (EDO): CRYO-PROTECTANT AGENT PROTOPORPHYRIN IX CONTAINING FE (HEM): HEME THIOLATE ...1,2-ETHANEDIOL | Sequence details | 6XHIS TAG IS ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 68 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 45% TACSIMATE, PH 7.0; 2% GLUCOSE; 0.1 M NA CACODYLATE |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2→80.32 Å / Num. obs: 46604 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 4.7 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2X5W Resolution: 2→76.5 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.364 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.121 / 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: 39.835 Å2
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Refinement step | Cycle: LAST / Resolution: 2→76.5 Å
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Refine LS restraints |
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