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- PDB-4pfd: Crystal structure of M. tuberculosis in complex with a cBT - non-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pfd | ||||||
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Title | Crystal structure of M. tuberculosis in complex with a cBT - non-covalent adduct | ||||||
![]() | Probable decaprenylphosphoryl-beta-D-ribose oxidase | ||||||
![]() | oxidoreductase/oxidoreductase inhibitor / DprE1 / ![]() ![]() | ||||||
Function / homology | ![]() arabinan biosynthetic process / cell wall polysaccharide biosynthetic process / decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Neres, J. / Panda, M. / Cole, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of M. tuberculosis in complex with a cBT Authors: Neres, J. / Cole, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.3 KB | Display | ![]() |
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PDB format | ![]() | 139.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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2 | ![]()
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Unit cell |
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Details | THE BIOLOGICAL ASSEMBLY IS UNKNOWN AS PER THE AUTHORS |
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Components
#1: Protein | Mass: 52260.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.03 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 34% polypropyleneglycol 400, 100 mM imidazole / PH range: 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2014 |
Radiation | Monochromator: Bartels monochromator with dual channel cut crystals Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→50 Å / Num. obs: 36486 / % possible obs: 97 % / Redundancy: 2.48 % / Net I/σ(I): 8.34 |
Reflection shell | Resolution: 2.3→2.33 Å / Redundancy: 2.51 % / Mean I/σ(I) obs: 2.32 / % possible all: 94.3 |
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Processing
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Refinement | Resolution: 2.3→48.02 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.254 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.419 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 34.463 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→48.02 Å
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Refine LS restraints |
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