[English] 日本語
Yorodumi- PDB-2pkm: Crystal structure of M tuberculosis Adenosine Kinase complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pkm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of M tuberculosis Adenosine Kinase complexed with adenosine | ||||||
Components | Adenosine kinase | ||||||
Keywords | TRANSFERASE / Mycobacterium tuberculosis / adenosine kinase / adenosine / 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 | 2pkm.cif.gz | 81.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2pkm.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 2pkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/2pkm ftp://data.pdbj.org/pub/pdb/validation_reports/pk/2pkm | HTTPS FTP |
---|
-Related structure data
Related structure data | 2pkfC 2pkkC 2pknC C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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: Rv2202 / Production host: Escherichia coli (E. coli) References: UniProt: P83734, UniProt: P9WID5*PLUS, adenosine kinase |
---|---|
#2: Chemical | ChemComp-ADN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.9 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Crystals were obtained in conditions containing 0.1 M HEPES-Na, pH 7.5 and 1.4 M trisodium citrate dihydrate, 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: Mar 5, 2006 / Details: Osmic mirrors |
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→62.66 Å / Num. all: 24855 / Num. obs: 24855 / % possible obs: 97.84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.04 |
Reflection shell | Resolution: 1.9→1.949 Å / % possible all: 97.33 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: apo MTB ADK Resolution: 1.9→62.26 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.878 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.167 / 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: 41.134 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→62.26 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|