+Open data
-Basic information
Entry | Database: PDB / ID: 1k44 | ||||||
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Title | Mycobacterium tuberculosis Nucleoside Diphosphate Kinase | ||||||
Components | Nucleoside Diphosphate KinaseNucleoside-diphosphate kinase | ||||||
Keywords | TRANSFERASE / Nucleoside Triphosphate / Nucleoside Diphosphate | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host innate immune response / purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / nuclease activity / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphoprotein phosphatase activity ...symbiont-mediated suppression of host innate immune response / purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / nuclease activity / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphoprotein phosphatase activity / Prevention of phagosomal-lysosomal fusion / phosphorylation / extracellular region / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Chen, Y. / Morera, S. / Lascu, I. / Janin, J. | ||||||
Citation | Journal: Proteins / Year: 2002 Title: X-ray structure of Mycobacterium tuberculosis nucleoside diphosphate kinase Authors: Chen, Y. / Morera, S. / Mocan, J. / Lascu, I. / Janin, J. #1: Journal: Structure / Year: 1995 Title: Nucleoside Diphosphate Kinase B Complexed with GDP at 2 A Resolution Authors: Morera, S. / Lacombe, M.L. / Xu, Y. / LeBras, G. / Janin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k44.cif.gz | 155.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k44.ent.gz | 126.3 KB | Display | PDB format |
PDBx/mmJSON format | 1k44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/1k44 ftp://data.pdbj.org/pub/pdb/validation_reports/k4/1k44 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14522.470 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: P84284, UniProt: P9WJH7*PLUS, nucleoside-diphosphate 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: 2.78 Å3/Da / Density % sol: 55.82 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG4000, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2001 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 30399 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.137 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 2978 / Rsym value: 0.46 / % possible all: 97.5 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 99.5 % / Redundancy: 5.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.205 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.205 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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