[English] 日本語
Yorodumi- PDB-2pkn: Crystal structure of M tuberculosis Adenosine Kinase complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pkn | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of M tuberculosis Adenosine Kinase complexed with AMP-PCP (non-hydrolyzable ATP analog) | ||||||
Components | Adenosine kinase | ||||||
Keywords | TRANSFERASE / Mycobacterium tuberculosis / adenosine kinase / Structural Genomics / TB Structural Genomics Consortium / TBSGC / PSI-2 / Protein Structure Initiative | ||||||
Function / homology | Function and homology information adenosine kinase / adenosine kinase activity / dGTP binding / AMP salvage / purine ribonucleoside salvage / phosphorylation / GTP binding / magnesium ion binding / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Reddy, M.C.M. / Palaninathan, S.K. / Shetty, N.D. / Owen, J.L. / Watson, M.D. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: High resolution crystal structures of Mycobacterium tuberculosis adenosine kinase: insights into the mechanism and specificity of this novel prokaryotic enzyme Authors: Reddy, M.C.M. / Palaninathan, S.K. / Shetty, N.D. / Owen, J.L. / Watson, M.D. / Sacchettini, J.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2pkn.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2pkn.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 2pkn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/2pkn ftp://data.pdbj.org/pub/pdb/validation_reports/pk/2pkn | HTTPS FTP |
---|
-Related structure data
Related structure data | 2pkfC 2pkkC 2pkmC C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 35683.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: adoK / Production host: Escherichia coli (E. coli) References: UniProt: P83734, UniProt: P9WID5*PLUS, adenosine kinase |
---|---|
#2: Chemical | ChemComp-ACP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.14 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 8000, 100 mM sodium cacodylate pH 6.5, and 200 mM magnesium acetate tetrahydrate , VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5412 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 2006 |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5412 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→57.54 Å / Num. all: 25991 / Num. obs: 25991 / % possible obs: 99.87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.05 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: apo MTB ADK Resolution: 1.9→57.54 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.016 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.161 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.41 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→57.54 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|