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- PDB-3v7w: 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: 3v7w | |||||||||
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Title | Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 5'-azido-5'-deoxyadenosine | |||||||||
![]() | Probable inorganic polyphosphate/ATP-NAD kinase 1 | |||||||||
![]() | TRANSFERASE / ligand-screening by crystallography / Two-domain kinase / Inorganic polyphosphate/ATP-NAD kinase 1 | |||||||||
Function / homology | ![]() NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / NAD metabolic process / NAD binding / phosphorylation / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Gelin, M. / Poncet-Montange, G. / Assairi, L. / Morellato, L. / Huteau, V. / Dugu, L. / Dussurget, O. / Pochet, S. / Labesse, G. | |||||||||
![]() | ![]() Title: Screening and In Situ Synthesis Using Crystals of a NAD Kinase Lead to a Potent Antistaphylococcal Compound. Authors: Gelin, M. / Poncet-Montange, G. / Assairi, L. / Morellato, L. / Huteau, V. / Dugue, L. / Dussurget, O. / Pochet, S. / Labesse, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125 KB | Display | ![]() |
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PDB format | ![]() | 97.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 992.9 KB | Display | ![]() |
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Full document | ![]() | 997 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3v7uC ![]() 3v7yC ![]() 3v80C ![]() 3v8mC ![]() 3v8nC ![]() 3v8pC ![]() 3v8qC ![]() 3v8rC 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
#1: Protein | Mass: 31045.279 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CIT / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.61 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 30 mM sodium bromide, 220 mM potassium citrate, pH 4.8-5.1, glycerol 6%, 15-16% w/v polyethylene glycol 400, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 12, 2007 |
Radiation | Monochromator: Asymmetric Laue 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→62.75 Å / Num. obs: 18364 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % |
Reflection shell | Resolution: 2.01→2.12 Å / Redundancy: 5.6 % / % possible all: 94 |
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Processing
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Refinement | Method to determine structure: Isomorphous replacement / Resolution: 2.0102→37.258 Å / SU ML: 0.26 / σ(F): 1.06 / Phase error: 21.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.879 Å2 / ksol: 0.345 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.0102→37.258 Å
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Refine LS restraints |
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LS refinement shell |
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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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