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Yorodumi- PDB-4otk: A structural characterization of the isoniazid Mycobacterium tube... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4otk | ||||||
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Title | A structural characterization of the isoniazid Mycobacterium tuberculosis drug target, Rv2971, in its unliganded form | ||||||
Components | Mycobacterial Enzyme Rv2971 | ||||||
Keywords | OXIDOREDUCTASE / TIM Barrel | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NADP+) activity / cell wall / Oxidoreductases / aldose reductase (NADPH) activity / oxidoreductase activity / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Shahine, A. / Beddoe, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2014 Title: A structural characterization of the isoniazid Mycobacterium tuberculosis drug target, Rv2971, in its unliganded form Authors: Shahine, A. / Prasetyoputri, A. / Rossjohn, J. / Beddoe, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4otk.cif.gz | 126.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4otk.ent.gz | 97 KB | Display | PDB format |
PDBx/mmJSON format | 4otk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/4otk ftp://data.pdbj.org/pub/pdb/validation_reports/ot/4otk | HTTPS FTP |
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-Related structure data
Related structure data | 2wztS 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: 34188.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv2971, MT3049 / Production host: Escherichia coli (E. coli) References: UniProt: P95124, UniProt: P9WQA5*PLUS, Oxidoreductases | ||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: 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: 2.71 Å3/Da / Density % sol: 54.63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2M Na-Malonate pH 5.0, 19% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 16, 2012 |
Radiation | Monochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→38.58 Å / Num. all: 49368 / Num. obs: 49368 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.6→1.66 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WZT Resolution: 1.6→38.58 Å / SU ML: 0.16 / σ(F): 1.33 / Phase error: 14.53 / 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: 1.6→38.58 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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