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Yorodumi- PDB-3e27: Nicotinic acid mononucleotide (NaMN) adenylyltransferase from Bac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3.0E+27 | ||||||
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Title | Nicotinic acid mononucleotide (NaMN) adenylyltransferase from Bacillus anthracis: product complex | ||||||
Components | Nicotinate (Nicotinamide) nucleotide adenylyltransferase | ||||||
Keywords | TRANSFERASE / Rossman-like fold / nucleotide-binding motif / Nucleotidyltransferase | ||||||
Function / homology | Function and homology information nicotinate-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Martynowski, D. / Eyobo, Y. / Zhang, H. | ||||||
Citation | Journal: Chem.Biol. / Year: 2009 Title: Targeting NAD biosynthesis in bacterial pathogens: Structure-based development of inhibitors of nicotinate mononucleotide adenylyltransferase NadD. Authors: Sorci, L. / Pan, Y. / Eyobo, Y. / Rodionova, I. / Huang, N. / Kurnasov, O. / Zhong, S. / MacKerell, A.D. / Zhang, H. / Osterman, A.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e27.cif.gz | 177.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e27.ent.gz | 142.4 KB | Display | PDB format |
PDBx/mmJSON format | 3e27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/3e27 ftp://data.pdbj.org/pub/pdb/validation_reports/e2/3e27 | HTTPS FTP |
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-Related structure data
Related structure data | 3hfjC 1kamS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21983.305 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: B. anthracis Ames / Gene: nadD, BT9727_4068 / Plasmid: a pET derived vector / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli BL21/DE3 References: UniProt: A0A2P0HJA8*PLUS, nicotinate-nucleotide adenylyltransferase #2: Chemical | ChemComp-DND / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: Osmic VariMax |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 43353 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 15.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1kam Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.551 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.75 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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