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Yorodumi- PDB-5eji: Crystal structure of NAD kinase W78F mutant from Listeria monocyt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eji | ||||||
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Title | Crystal structure of NAD kinase W78F mutant from Listeria monocytogenes in complex with NADP/Mn++/PPi | ||||||
Components | NAD kinase 1NAD+ kinase | ||||||
Keywords | TRANSFERASE / Gram-positive NAD Kinase / allostery / citrate | ||||||
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 / Resolution: 2.292 Å | ||||||
Authors | Poncet-Montange, G. / Assairi, L. / Gelin, M. / Pochet, S. / Labesse, G. | ||||||
Funding support | France, 1items
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Citation | Journal: to be published Title: Crystal structure of NAD kinase W78F mutant from Listeria monocytogenes in complex with NADP/Mn++/PPi Authors: Poncet-Montange, G. / Assairi, L. / Gelin, M. / Pochet, S. / Labesse, G. #1: Journal: To Be Published Title: Molecular basis of NAD kinase catalysis reveals citrate is an allosteric regulator. Authors: Poncet-Montange, G. / Assairi, L. / Gelin, M. / 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 | 5eji.cif.gz | 115.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eji.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 5eji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/5eji ftp://data.pdbj.org/pub/pdb/validation_reports/ej/5eji | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 31006.244 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: nadK1, lmo0968 / Plasmid: pLA15.3.3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Y8D7, NAD+ kinase |
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-Non-polymers , 5 types, 38 molecules
#2: Chemical | ChemComp-NAP / |
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#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-POP / |
#5: Chemical | ChemComp-CIT / |
#6: 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: 45.7 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 50 mM Sodium Bromide, 150 mM tri-sodium citrate dihydrate, pH 5.1-5.4, 14-16% w/v polyethylene glycol 400 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.829→63.069 Å / Num. all: 13007 / Num. obs: 13007 / % possible obs: 100 % / Redundancy: 4.1 % / Rpim(I) all: 0.039 / Rrim(I) all: 0.079 / Rsym value: 0.061 / Net I/av σ(I): 9.5 / Net I/σ(I): 12.5 / Num. measured all: 53269 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Resolution: 2.292→63.08 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 29.86 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.75 Å2 / Biso mean: 56.6136 Å2 / Biso min: 13.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.292→63.08 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / 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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