[English] 日本語
Yorodumi- PDB-1nsy: CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nsy | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS | ||||||
Components | NAD SYNTHETASE | ||||||
Keywords | 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 Å | ||||||
Authors | Rizzi, M. / Nessi, C. / Bolognesi, M. / Galizzi, A. / Coda, A. | ||||||
Citation | Journal: EMBO J. / Year: 1996 Title: Crystal structure of NH3-dependent NAD+ synthetase from Bacillus subtilis. Authors: Rizzi, M. / Nessi, C. / Mattevi, A. / Coda, A. / Bolognesi, M. / Galizzi, A. #1: Journal: Proteins / Year: 1996 Title: Crystallization of Nad+ Synthetase from Bacillus Subtilis Authors: Rizzi, M. / Nessi, C. / Bolognesi, M. / Coda, A. / Galizzi, A. #2: Journal: J.Biol.Chem. / Year: 1995 Title: The Outb Gene of Bacillus Subtilis Codes for Nad Synthetase Authors: Nessi, C. / Albertini, A.M. / Speranza, M.L. / Galizzi, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1nsy.cif.gz | 125.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1nsy.ent.gz | 97.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nsy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/1nsy ftp://data.pdbj.org/pub/pdb/validation_reports/ns/1nsy | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30303.994 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) References: UniProt: P08164, NAD+ synthase (glutamine-hydrolysing) |
---|
-Non-polymers , 5 types, 233 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 28 ℃ / pH: 5.2 / Method: microdialysis | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Wavelength: 1.5418 |
---|---|
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 5, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 33464 / % possible obs: 94 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.064 |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 177041 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→15 Å / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.174 / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→15 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.174 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |