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Yorodumi- PDB-4nxi: Rv2466c Mediates the Activation of TP053 To Kill Replicating and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nxi | ||||||
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Title | Rv2466c Mediates the Activation of TP053 To Kill Replicating and Non-replicating Mycobacterium tuberculosis | ||||||
Components | Uncharacterized protein | ||||||
Keywords | OXIDOREDUCTASE / thioredoxin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 Å | ||||||
Authors | Albesa-Jove, D. / Urresti, S. / Comino, N. / Guerin, M.E. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2014 Title: Rv2466c mediates the activation of TP053 to kill replicating and non-replicating Mycobacterium tuberculosis. Authors: Albesa-Jove, D. / Chiarelli, L.R. / Makarov, V. / Pasca, M.R. / Urresti, S. / Mori, G. / Salina, E. / Vocat, A. / Comino, N. / Mohorko, E. / Ryabova, S. / Pfieiffer, B. / Lopes Ribeiro, A.L. ...Authors: Albesa-Jove, D. / Chiarelli, L.R. / Makarov, V. / Pasca, M.R. / Urresti, S. / Mori, G. / Salina, E. / Vocat, A. / Comino, N. / Mohorko, E. / Ryabova, S. / Pfieiffer, B. / Lopes Ribeiro, A.L. / Rodrigo-Unzueta, A. / Tersa, M. / Zanoni, G. / Buroni, S. / Altmann, K.H. / Hartkoorn, R.C. / Glockshuber, R. / Cole, S.T. / Riccardi, G. / Guerin, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nxi.cif.gz | 100.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nxi.ent.gz | 75.9 KB | Display | PDB format |
PDBx/mmJSON format | 4nxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nxi_validation.pdf.gz | 451.9 KB | Display | wwPDB validaton report |
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Full document | 4nxi_full_validation.pdf.gz | 453.5 KB | Display | |
Data in XML | 4nxi_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 4nxi_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/4nxi ftp://data.pdbj.org/pub/pdb/validation_reports/nx/4nxi | HTTPS FTP |
-Related structure data
Related structure data | 2imeS S: Starting model for refinement |
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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: 23120.059 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: RVBD_2466c / Production host: Escherichia coli (E. coli) / References: UniProt: O53193 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M TRIS pH 8.5, 0.20M MgCl2, 30% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9724 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2013 |
Radiation | Monochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 1.698→39.664 Å / Num. all: 38501 / Num. obs: 36376 / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 14.38 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3069 / % possible all: 80.24 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IME Resolution: 1.698→39.66 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 18.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.698→39.66 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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