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- PDB-2x5l: 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: 2x5l | ||||||
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Title | X-RAY STRUCTURE OF THE SUBSTRATE-FREE MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 CYP125, ALTERNATIVE CRYSTAL FORM | ||||||
![]() | PUTATIVE CYTOCHROME P450 125 | ||||||
![]() | OXIDOREDUCTASE / CHOLESTEROL DEGRADATION / MONOOXYGENASE / METAL-BINDING | ||||||
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 | ![]() | 211.4 KB | Display | ![]() |
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PDB format | ![]() | 168.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 779.8 KB | Display | ![]() |
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Full document | ![]() | 788.4 KB | Display | |
Data in XML | ![]() | 25.8 KB | Display | |
Data in CIF | ![]() | 40.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xc3C ![]() 2xn8C ![]() 3ivyS 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: 48330.383 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-433 / Mutation: YES Source method: isolated from a genetically manipulated source 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-HEM / | ||||
#3: Water | ChemComp-HOH / | ||||
Compound details | ENGINEEREDNonpolymer details | PROTOPORPH | Sequence details | FIRST 16 RESIDUES UPSTREAM OF V17 ARE TRUNCATED. MUTATIONS V17M AND C429L WERE ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.7 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M AMMONIUM ACETATE, 0.1 M BIS-TRIS, PH 5.5, 17% PEG 10000 AT 4 C |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 15, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→102.6 Å / Num. obs: 66632 / % possible obs: 94.9 % / Observed criterion σ(I): 1.5 / Redundancy: 4.1 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.48→1.56 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.5 / % possible all: 71.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3IVY Resolution: 1.48→102.22 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.786 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.079 / 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: 18.624 Å2
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Refinement step | Cycle: LAST / Resolution: 1.48→102.22 Å
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Refine LS restraints |
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