+Open data
-Basic information
Entry | Database: PDB / ID: 2pkf | ||||||
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Title | Crystal structure of M tuberculosis Adenosine Kinase (apo) | ||||||
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 / ketohexokinase activity / regulation of glycogen metabolic process / dGTP binding / response to sucrose / response to fructose / AMP salvage / fructose metabolic process / purine ribonucleoside salvage ...adenosine kinase / adenosine kinase activity / ketohexokinase activity / regulation of glycogen metabolic process / dGTP binding / response to sucrose / response to fructose / AMP salvage / fructose metabolic process / purine ribonucleoside salvage / response to zinc ion / response to glucose / response to insulin / GTP binding / magnesium ion binding / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pkf.cif.gz | 159.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pkf.ent.gz | 124.8 KB | Display | PDB format |
PDBx/mmJSON format | 2pkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/2pkf ftp://data.pdbj.org/pub/pdb/validation_reports/pk/2pkf | HTTPS FTP |
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-Related structure data
Related structure data | 2pkkC 2pkmC 2pknC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 2 - 324 / Label seq-ID: 12 - 334
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-Components
#1: Protein | Mass: 35683.164 Da / Num. of mol.: 2 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: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.63 % |
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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: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2005 |
Radiation | Monochromator: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geometry Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→81.11 Å / Num. all: 104080 / Num. obs: 104080 / % possible obs: 99.77 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.04 |
Reflection shell | Resolution: 1.5→1.53 Å / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Se-met MAD low resolution structure Resolution: 1.5→81.11 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.184 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 18.532 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→81.11 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2412 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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