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Yorodumi- PDB-3v8q: Crystal structure of NAD kinase 1 H223E mutant from Listeria mono... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v8q | ||||||
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Title | Crystal structure of NAD kinase 1 H223E mutant from Listeria monocytogenes in complex with 5'-amino-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: 2.37 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 | 3v8q.cif.gz | 125 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v8q.ent.gz | 97.2 KB | Display | PDB format |
PDBx/mmJSON format | 3v8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v8q_validation.pdf.gz | 757 KB | Display | wwPDB validaton report |
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Full document | 3v8q_full_validation.pdf.gz | 762.4 KB | Display | |
Data in XML | 3v8q_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 3v8q_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/3v8q ftp://data.pdbj.org/pub/pdb/validation_reports/v8/3v8q | HTTPS FTP |
-Related structure data
Related structure data | 3v7uC 3v7wC 3v7yC 3v80C 3v8mC 3v8nC 3v8pC 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: 31036.244 Da / Num. of mol.: 1 / Mutation: H233E 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-5N5 / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-CIT / |
#5: 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: 2.26 Å3/Da / Density % sol: 45.67 % |
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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: ID14-1 / Wavelength: 0.9334 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 10, 2009 |
Radiation | Monochromator: Asymmetric Laue 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→48.45 Å / Num. obs: 11844 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % |
Reflection shell | Resolution: 2.29→2.41 Å / Redundancy: 4 % / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: Isomorphous replacement / Resolution: 2.37→48.331 Å / SU ML: 0.32 / σ(F): 1.36 / Phase error: 26.85 / 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: 73.457 Å2 / ksol: 0.353 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.37→48.331 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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