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- PDB-1ifx: CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS ... -
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Open data
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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 | ||||||
![]() | NH(3)-DEPENDENT NAD(+) SYNTHETASE | ||||||
![]() | LIGASE / LYASE / AMIDOTRANSFERASE / NH3 DEPENDENT / ATP / PYROPHOSPHATASE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Devedjiev, Y. / Symersky, J. / Singh, R. / Brouillette, W. / Muccio, D. / Jedrzejas, M. / Brouillette, C. / DeLucas, L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.8 KB | Display | ![]() |
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PDB format | ![]() | 88.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 922.4 KB | Display | ![]() |
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Full document | ![]() | 936 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 33.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ee1SC ![]() 1fydC ![]() 1ih8C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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 |
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Components
#1: Protein | Mass: 30303.994 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P08164, NAD+ synthase (glutamine-hydrolysing) #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 % |
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Processing
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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: ![]() | |||||||||||||||||||||||||||
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 |