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Yorodumi- PDB-3v7y: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v7y | ||||||
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Title | Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 5'-N-Propargylamino-5'-deoxyadenosine | ||||||
Components | Probable inorganic polyphosphate/ATP-NAD kinase 1 | ||||||
Keywords | TRANSFERASE / ligand-screening by crystallography / Two-domain kinase / Inorganic polyphosphate/ATP-NAD kinase 1 | ||||||
Function / homology | Function and homology information NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / NAD metabolic process / NAD binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Isomorphous replacement / Resolution: 1.97 Å | ||||||
Authors | Gelin, M. / Poncet-Montange, G. / Assairi, L. / Morellato, L. / Huteau, V. / Dugu, L. / Dussurget, O. / Pochet, S. / Labesse, G. | ||||||
Citation | Journal: Structure / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v7y.cif.gz | 125.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v7y.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 3v7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v7y_validation.pdf.gz | 991.4 KB | Display | wwPDB validaton report |
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Full document | 3v7y_full_validation.pdf.gz | 997.2 KB | Display | |
Data in XML | 3v7y_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 3v7y_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/3v7y ftp://data.pdbj.org/pub/pdb/validation_reports/v7/3v7y | HTTPS FTP |
-Related structure data
Related structure data | 3v7uC 3v7wC 3v80C 3v8mC 3v8nC 3v8pC 3v8qC 3v8rC C: citing same article (ref.) |
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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 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.) Listeria monocytogenes (bacteria) / Gene: ppnK1, lmo0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase | ||
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#2: Chemical | ChemComp-CIT / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.82 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979338 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2011 |
Radiation | Monochromator: Asymmetric Laue 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979338 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→48.34 Å / Num. obs: 20293 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % |
Reflection shell | Resolution: 1.97→2.08 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: Isomorphous replacement / Resolution: 1.97→48.332 Å / SU ML: 0.32 / σ(F): 1.06 / Phase error: 26.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.342 Å2 / ksol: 0.348 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.97→48.332 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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