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Yorodumi- PDB-4pfd: Crystal structure of M. tuberculosis in complex with a cBT - non-... -
+Open data
-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 | ||||||
Components | Probable decaprenylphosphoryl-beta-D-ribose oxidase | ||||||
Keywords | oxidoreductase/oxidoreductase inhibitor / DprE1 / inhibitor / covalent / oxidoreductase-oxidoreductase inhibitor complex | ||||||
Function / homology | Function and homology information arabinan biosynthetic process / cell wall polysaccharide biosynthetic process / decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / oxidoreductase activity / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Neres, J. / Panda, M. / Cole, S. | ||||||
Funding support | 1items
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Citation | Journal: To be published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pfd.cif.gz | 180.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pfd.ent.gz | 139.4 KB | Display | PDB format |
PDBx/mmJSON format | 4pfd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pfd_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4pfd_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4pfd_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 4pfd_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/4pfd ftp://data.pdbj.org/pub/pdb/validation_reports/pf/4pfd | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-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 |
-Components
#1: Protein | Mass: 52260.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: dprE1, Rv3790 / Plasmid: pET28a / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P9WJF1, Oxidoreductases #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
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: 1 Å / Relative weight: 1 |
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 |
-Processing
Software |
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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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