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Yorodumi- PDB-4f4q: Crystal structure of M. smegmatis DprE1 in complex with FAD and c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f4q | ||||||
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Title | Crystal structure of M. smegmatis DprE1 in complex with FAD and covalently bound BTZ043 | ||||||
Components | DprE1 | ||||||
Keywords | OXIDOREDUCTASE / FAD domain / oxidase / BTZ043 covalently bound to Cys394 | ||||||
Function / homology | Function and homology information decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / response to antibiotic / membrane Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.619 Å | ||||||
Authors | Neres, J. / Pojer, F. / Molteni, E. / Chiarelli, L. / Riccardi, G. / Mattevi, A. / Cole, S.T. / Binda, C. | ||||||
Citation | Journal: Sci Transl Med / Year: 2012 Title: Structural Basis for Benzothiazinone-Mediated Killing of Mycobacterium tuberculosis. Authors: Neres, J. / Pojer, F. / Molteni, E. / Chiarelli, L.R. / Dhar, N. / Boy-Rottger, S. / Buroni, S. / Fullam, E. / Degiacomi, G. / Lucarelli, A.P. / Read, R.J. / Zanoni, G. / Edmondson, D.E. / ...Authors: Neres, J. / Pojer, F. / Molteni, E. / Chiarelli, L.R. / Dhar, N. / Boy-Rottger, S. / Buroni, S. / Fullam, E. / Degiacomi, G. / Lucarelli, A.P. / Read, R.J. / Zanoni, G. / Edmondson, D.E. / De Rossi, E. / Pasca, M.R. / McKinney, J.D. / Dyson, P.J. / Riccardi, G. / Mattevi, A. / Cole, S.T. / Binda, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f4q.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f4q.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 4f4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/4f4q ftp://data.pdbj.org/pub/pdb/validation_reports/f4/4f4q | HTTPS FTP |
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-Related structure data
Related structure data | 4autSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 51190.887 Da / Num. of mol.: 1 / Fragment: DprE1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_6382 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R607 |
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#2: Chemical | ChemComp-0SK / |
#3: Chemical | ChemComp-FAD / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 11% PEG 300, 90 mM MES pH 5.9, 5% tetrabutylammonium bromide, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: PILATUS 2M-F detector / Detector: PIXEL / Date: Feb 13, 2012 |
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: 2.619→50 Å / Num. all: 16323 / Num. obs: 16323 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.619→2.78 Å / Redundancy: 4.33 % / Mean I/σ(I) obs: 2.45 / Num. unique all: 4463 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AUT Resolution: 2.619→46.6 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.476 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.685 / ESU R Free: 0.3 / 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: 35.526 Å2
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Refinement step | Cycle: LAST / Resolution: 2.619→46.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.619→2.687 Å / Total num. of bins used: 20
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