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- PDB-4ktk: Crystal structure of Mycobacterium tuberculosis CYP121 in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ktk | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis CYP121 in complex with 4-(3-amino-4-(4-hydroxyphenyl)-1H-pyrazol-5-yl)benzene-1,3-diol | ||||||
![]() | Cytochrome P450 121 | ||||||
![]() | OXIDOREDUCTASE / P450 / cYY / C-C bond formation / Assumed cytosol | ||||||
Function / homology | Cytochrome p450 / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha / PROTOPORPHYRIN IX CONTAINING FE / Chem-KTK / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hudson, S.A. | ||||||
![]() | ![]() Title: Overcoming the Limitations of Fragment Merging: Rescuing a Strained Merged Fragment Series Targeting Mycobacterium tuberculosis CYP121. Authors: Hudson, S.A. / Surade, S. / Coyne, A.G. / McLean, K.J. / Leys, D. / Munro, A.W. / Abell, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106 KB | Display | ![]() |
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PDB format | ![]() | 78.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 34.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ktfC ![]() 4ktjC ![]() 4ktlC ![]() 1n40S 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 on special symmetry positions |
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Components
#1: Protein | Mass: 43174.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: I6YD01, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 2M Ammonium sulfate, 0.1M Sodium cacodylate-HCl, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jul 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91731 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→38.88 Å / Num. all: 76131 / Num. obs: 76131 / % possible obs: 82.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 9977 / % possible all: 75.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1N40 Resolution: 1.4→38.47 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.854 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.059 / ESU R Free: 0.063 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.951 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→38.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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