+Open data
-Basic information
Entry | Database: PDB / ID: 2i2d | ||||||
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Title | Crystal structure of LmNADK1 | ||||||
Components | Probable inorganic polyphosphate/ATP-NAD kinase 1 | ||||||
Keywords | TRANSFERASE / Crystal structure of LmNADK1 bound to a NAD analog | ||||||
Function / homology | Function and homology information 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 | Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | ||||||
Authors | Poncet-Montange, G. / Labesse, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: NAD kinases use substrate-assisted catalysis for specific recognition of NAD. Authors: Poncet-Montange, G. / Assairi, L. / Arold, S. / 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 | 2i2d.cif.gz | 68.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i2d.ent.gz | 49.6 KB | Display | PDB format |
PDBx/mmJSON format | 2i2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/2i2d ftp://data.pdbj.org/pub/pdb/validation_reports/i2/2i2d | HTTPS FTP |
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-Related structure data
Related structure data | 2i1wC 2i29C 2i2aC 2i2bSC 2i2cC 2i2fC 2q5fC 4dy6C C: citing same article (ref.) S: Starting model for refinement |
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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) / Strain: Bacteria / Gene: ppnK1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase |
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#2: Chemical | ChemComp-A2D / |
#3: Chemical | ChemComp-CIT / |
#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: 2.34 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.3 M potassium chloride, 50 mM tri-sodium citrate dihydrate, 15-20% w/v polyethylene glycol 400, pH 5.4, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→37.9 Å / Num. all: 13780 / Num. obs: 13383 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.22→2.34 Å / Redundancy: 4 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 3.5 / % possible all: 81.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2i2b Resolution: 2.22→37.93 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.595 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.306 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.883 Å2
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Refinement step | Cycle: LAST / Resolution: 2.22→37.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.22→2.277 Å / Total num. of bins used: 20
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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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