[English] 日本語
Yorodumi- PDB-4bfs: Crystal structure of Mycobacterium tuberculosis PanK in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bfs | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium tuberculosis PanK in complex with a triazole inhibitory compound (1a) | ||||||
Components | PANTOTHENATE KINASE | ||||||
Keywords | TRANSFERASE / COA PATHWAY / INHIBITOR | ||||||
Function / homology | Function and homology information pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Bjorkelid, C. / Bergfors, T. / Jones, T.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural and Biochemical Characterization of Compounds Inhibiting Mycobacterium Tuberculosis Pank Authors: Bjorkelid, C. / Bergfors, T. / Raichurkar, A.K.V. / Mukherjee, K. / Krishnan, M. / Bandodkar, B. / Jones, T.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4bfs.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4bfs.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 4bfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/4bfs ftp://data.pdbj.org/pub/pdb/validation_reports/bf/4bfs | HTTPS FTP |
---|
-Related structure data
Related structure data | 4bftC 4bfuC 4bfvC 4bfwC 4bfxC 4bfyC 4bfzC 2gevS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36533.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P63810, UniProt: P9WPA7*PLUS, pantothenate kinase |
---|---|
#2: Chemical | ChemComp-ZVS / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.07 Å3/Da / Density % sol: 69.83 % / Description: NONE |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. 14.4% (W/V) PEG 8000, 20% (V/V) GLYCEROL, 0.08 M SODIUM CACODYLATE, PH 6.5, AND 0.16 M CALCIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04123 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 6, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04123 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. obs: 13018 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.3 / % possible all: 99.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GEV Resolution: 2.9→28.74 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.64 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.589 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 54.855 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→28.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|