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Yorodumi- PDB-1kaq: Structure of Bacillus subtilis Nicotinic Acid Mononucleotide Aden... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kaq | ||||||
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Title | Structure of Bacillus subtilis Nicotinic Acid Mononucleotide Adenylyl Transferase | ||||||
Components | NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / Rossmann fold / NaAD | ||||||
Function / homology | Function and homology information nicotinate-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Combined MAD, molecular replacement phases / Resolution: 3.2 Å | ||||||
Authors | Olland, A.M. / Underwood, K.W. / Czerwinski, R.M. / Lo, M.C. / Aulabaugh, A. / Bard, J. / Stahl, M.L. / Somers, W.S. / Sullivan, F.X. / Chopra, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Identification, characterization, and crystal structure of Bacillus subtilis nicotinic acid mononucleotide adenylyltransferase. Authors: Olland, A.M. / Underwood, K.W. / Czerwinski, R.M. / Lo, M.C. / Aulabaugh, A. / Bard, J. / Stahl, M.L. / Somers, W.S. / Sullivan, F.X. / Chopra, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kaq.cif.gz | 232.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kaq.ent.gz | 190.4 KB | Display | PDB format |
PDBx/mmJSON format | 1kaq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/1kaq ftp://data.pdbj.org/pub/pdb/validation_reports/ka/1kaq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 22618.902 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: nadD / Plasmid: pML208 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P54455, nicotinate-nucleotide adenylyltransferase #2: Chemical | ChemComp-DND / |
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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: 2.78 Å3/Da / Density % sol: 55.83 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3350, Magnesium Acetate, xylitol, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9791, 0.9639 | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2001 | |||||||||
Radiation | Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 3.2→15 Å / Num. all: 25491 / Num. obs: 24599 / % possible obs: 96.5 % / Observed criterion σ(I): 2 | |||||||||
Reflection shell | Resolution: 3.2→3.31 Å / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 5.6 / Num. unique all: 1920 / % possible all: 84 | |||||||||
Reflection | *PLUS Highest resolution: 3.2 Å / Num. measured all: 80499 / Rmerge(I) obs: 0.147 | |||||||||
Reflection shell | *PLUS % possible obs: 84 % / Rmerge(I) obs: 0.289 |
-Processing
Software |
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Refinement | Method to determine structure: Combined MAD, molecular replacement phases Resolution: 3.2→15 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.23 Å
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Refinement | *PLUS Highest resolution: 3.2 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.2975 / Rfactor Rwork: 0.2564 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.3379 / Rfactor Rwork: 0.3957 |