[English] 日本語
Yorodumi- PDB-4bfx: Crystal structure of Mycobacterium tuberculosis PanK in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bfx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium tuberculosis PanK in complex with a triazole inhibitory compound (1f) and phosphate | ||||||
Components | PANTOTHENATE KINASE | ||||||
Keywords | TRANSFERASE / COA PATHWAY | ||||||
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: 2.7 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 | 4bfx.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4bfx.ent.gz | 109.2 KB | Display | PDB format |
PDBx/mmJSON format | 4bfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/4bfx ftp://data.pdbj.org/pub/pdb/validation_reports/bf/4bfx | HTTPS FTP |
---|
-Related structure data
Related structure data | 4bfsC 4bftC 4bfuC 4bfvC 4bfwC 4bfyC 4bfzC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 36533.727 Da / Num. of mol.: 2 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 | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.59 % / Description: NONE |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. 1.8 M SODIUM/POTASSIUM PHOSPHATE, PH 8.2 |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 7, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→60 Å / Num. obs: 23491 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BFX Resolution: 2.7→57.04 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.889 / SU B: 14.008 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 0.912 / ESU R Free: 0.375 / 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: 45.602 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→57.04 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|