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- PDB-6rgd: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rgd | ||||||
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Title | Crystal structure of NAD kinase 1 from Listeria monocytogenes in complexe with an inhibitor | ||||||
![]() | NAD kinase 1 | ||||||
![]() | TRANSFERASE / tetrameric NAD kinase | ||||||
Function / homology | ![]() NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / NAD metabolic process / NAD binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gelin, M. / Labesse, G. | ||||||
![]() | ![]() Title: From Substrate to Fragments to Inhibitor ActiveIn VivoagainstStaphylococcus aureus. Authors: Gelin, M. / Paoletti, J. / Nahori, M.A. / Huteau, V. / Leseigneur, C. / Jouvion, G. / Dugue, L. / Clement, D. / Pons, J.L. / Assairi, L. / Pochet, S. / Labesse, G. / Dussurget, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.8 KB | Display | ![]() |
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PDB format | ![]() | 93.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6rboC ![]() 6rbpC ![]() 6rbqC ![]() 6rbrC ![]() 6rbsC ![]() 6rbtC ![]() 6rbuC ![]() 6rbvC ![]() 6rbwC ![]() 6rbxC ![]() 6rbyC ![]() 6rbzC ![]() 6rc0C ![]() 6rc1C ![]() 6rc2C ![]() 6rc3C ![]() 6rc4C ![]() 6rc5C ![]() 6rc6C ![]() 6rg6C ![]() 6rg7C ![]() 6rg8C ![]() 6rg9C ![]() 6rgaC ![]() 6rgbC ![]() 6rgcC ![]() 6rr2C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 31045.279 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: nadK1, lmo0968 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-CIT / |
#3: Chemical | ChemComp-K2W / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.88 % / Mosaicity: 1.12 ° |
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Crystal grow | Temperature: 291.15 K / Method: evaporation / pH: 5 Details: 30 mM NaBr, 220 mM Kcitrate, glycerol 6%, 15-16% w/v PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 12, 2012 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→59.48 Å / Num. obs: 12634 / % possible obs: 98.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 44.82 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.039 / Rrim(I) all: 0.071 / Net I/σ(I): 10.9 / Num. measured all: 39273 / Scaling rejects: 62 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 117.68 Å2 / Biso mean: 55.4093 Å2 / Biso min: 28.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→35.053 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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