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Yorodumi- PDB-6rbs: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rbs | ||||||
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Title | Crystal structure of NAD kinase 1 from Listeria monocytogenes in complexe with an adenine derivative | ||||||
Components | NAD kinase 1 | ||||||
Keywords | TRANSFERASE / tetrameric NAD kinase | ||||||
Function / homology | Function and homology information NAD+ kinase / NAD+ kinase activity / NADP biosynthetic process / NAD metabolic process / NAD binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Listeria monocytogenes serovar 1/2a (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.324 Å | ||||||
Authors | Gelin, M. / Labesse, G. | ||||||
Citation | Journal: Acs Infect Dis. / Year: 2020 Title: From Substrate to Fragments to Inhibitor ActiveIn VivoagainstStaphylococcus aureus. Authors: Gelin, M. / Paoletti, J. / Nahori, M.A. / Huteau, V. / Leseigneur, C. / Jouvion, G. / Dugue, L. / Clement, D. / Pons, J.L. / Assairi, L. / Pochet, S. / Labesse, G. / Dussurget, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rbs.cif.gz | 119.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rbs.ent.gz | 91.6 KB | Display | PDB format |
PDBx/mmJSON format | 6rbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rbs_validation.pdf.gz | 715.8 KB | Display | wwPDB validaton report |
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Full document | 6rbs_full_validation.pdf.gz | 717 KB | Display | |
Data in XML | 6rbs_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 6rbs_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/6rbs ftp://data.pdbj.org/pub/pdb/validation_reports/rb/6rbs | HTTPS FTP |
-Related structure data
Related structure data | 6rboC 6rbpC 6rbqC 6rbrC 6rbtC 6rbuC 6rbvC 6rbwC 6rbxC 6rbyC 6rbzC 6rc0C 6rc1C 6rc2C 6rc3C 6rc4C 6rc5C 6rc6C 6rg6C 6rg7C 6rg8C 6rg9C 6rgaC 6rgbC 6rgcC 6rgdC 6rr2C 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
#1: Protein | Mass: 31045.279 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria) Gene: nadK1, lmo0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase |
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#2: Chemical | ChemComp-CIT / |
#3: Chemical | ChemComp-JXT / |
#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: 2.28 Å3/Da / Density % sol: 46.08 % |
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Crystal grow | Temperature: 291.15 K / Method: evaporation / pH: 5 Details: 30 mM NaBr, 220 mM Kcitrate, glycerol 6%, 15-16% w/v PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 7, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.822→64.277 Å / Num. obs: 13646 / % possible obs: 92.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 47.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.032 / Rrim(I) all: 0.076 / Net I/σ(I): 14.2 / Num. measured all: 73857 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.324→35.075 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.06 Å2 / Biso mean: 58.0999 Å2 / Biso min: 30.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.324→35.075 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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Refinement TLS params. | S33: 0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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