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- PDB-2xn8: X-RAY STRUCTURE OF THE SUBSTRATE-FREE MYCOBACTERIUM TUBERCULOSIS ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xn8 | ||||||
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Title | X-RAY STRUCTURE OF THE SUBSTRATE-FREE MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 CYP125 | ||||||
![]() | PUTATIVE CYTOCHROME P450 125 | ||||||
![]() | OXIDOREDUCTASE / CHOLESTEROL DEGRADATION / REVERSE TYPE I INHIBITOR / MONOOXYGENASE | ||||||
Function / homology | ![]() cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / biological process involved in interaction with host / 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 | ![]() ![]() ![]() | ||||||
![]() | Ouellet, H. / Kells, P.M. / Ortiz de Montellano, P.R. / Podust, L.M. | ||||||
![]() | ![]() Title: Reverse Type I Inhibitor of Mycobacteriumtuberculosis Cyp125A1. Authors: Ouellet, H. / Kells, P.M. / Ortiz de Montellano, P.R. / Podust, L.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197.6 KB | Display | ![]() |
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PDB format | ![]() | 154.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 786.9 KB | Display | ![]() |
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Full document | ![]() | 791.5 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2x5lSC ![]() 2xc3C C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 47462.316 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-433 / Mutation: YES Source method: isolated from a genetically manipulated source Details: FIRST 16 RESIDUES UPSTREAM OF V17 ARE TRUNCATED. 6XHIS TAG IS ENGINEERED AT THE N-TERMINUS Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P63709, UniProt: P9WPP1*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-HEM / | ||
#4: Water | ChemComp-HOH / | ||
Nonpolymer details | PROTOPORPHSequence details | FIRST 16 RESIDUES UPSTREAM OF V17 ARE TRUNCATED. MUTATIONS V17M AND C429L ARE ENGINEERED. 6XHIS TAG ...FIRST 16 RESIDUES UPSTREAM OF V17 ARE TRUNCATED. MUTATIONS V17M AND C429L ARE ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 8.5 Details: 2.0M AMMONIUM SULFATE, 0.1 M TRIS-HCL, PH 8.5, 4 DEG. CELSIUS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 24, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→15.53 Å / Num. obs: 46349 / % possible obs: 99 % / Observed criterion σ(I): 1.5 / Redundancy: 6.1 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.64→1.73 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.2 / % possible all: 94.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2X5L Resolution: 1.64→58.3 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.989 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 234-235 AND 248-249 ARE DISORDERED
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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: 15.975 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→58.3 Å
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Refine LS restraints |
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