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Yorodumi- PDB-1ifx: CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ifx | ||||||
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Title | CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH TWO MOLECULES DEAMIDO-NAD | ||||||
Components | NH(3)-DEPENDENT NAD(+) SYNTHETASE | ||||||
Keywords | LIGASE / LYASE / AMIDOTRANSFERASE / NH3 DEPENDENT / ATP / PYROPHOSPHATASE | ||||||
Function / homology | Function and homology information NAD+ synthase / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD biosynthetic process / sporulation resulting in formation of a cellular spore / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.25 Å | ||||||
Authors | Devedjiev, Y. / Symersky, J. / Singh, R. / Brouillette, W. / Muccio, D. / Jedrzejas, M. / Brouillette, C. / DeLucas, L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis. Authors: Devedjiev, Y. / Symersky, J. / Singh, R. / Jedrzejas, M. / Brouillette, C. / Brouillette, W. / Muccio, D. / Chattopadhyay, D. / DeLucas, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ifx.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ifx.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ifx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/1ifx ftp://data.pdbj.org/pub/pdb/validation_reports/if/1ifx | HTTPS FTP |
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-Related structure data
Related structure data | 1ee1SC 1fydC 1ih8C 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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1 |
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis |
-Components
#1: Protein | Mass: 30303.994 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: NadE / Production host: Escherichia coli (E. coli) References: UniProt: P08164, NAD+ synthase (glutamine-hydrolysing) #2: Chemical | #3: 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: 2.15 Å3/Da / Density % sol: 42.67 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: sodium acetate buffer, Magnesium chloride, PEG 400, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 3, 1998 / Details: mirrors |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→25 Å / Num. all: 84706 / Num. obs: 24270 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2401 / Rsym value: 31.8 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 162585 |
Reflection shell | *PLUS % possible obs: 79.2 % |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1ee1 Resolution: 2.25→8 Å / σ(F): 2 / Stereochemistry target values: Engh, Huber
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Refinement step | Cycle: LAST / Resolution: 2.25→8 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree: 0.297 / Rfactor Rwork: 0.177 / Total num. of bins used: 8 / % reflection obs: 99 %
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.216 | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 4.3 Å / Lowest resolution: 8 Å / Rfactor Rfree: 0.297 / Rfactor Rwork: 0.177 |