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- PDB-1kqp: NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTION -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kqp | ||||||
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Title | NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTION | ||||||
![]() | NH(3)-dependent NAD(+) synthetase | ||||||
![]() | LIGASE / AMIDOTRANSFERASE / ATP PYROPHOSPHATASE / NAD-ADENYLATE | ||||||
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 | ![]() ![]() | ||||||
![]() | Symersky, J. / Devedjiev, Y. / Moore, K. / Brouillette, C. / DeLucas, L. | ||||||
![]() | ![]() Title: NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution. Authors: Symersky, J. / Devedjiev, Y. / Moore, K. / Brouillette, C. / DeLucas, L. #1: ![]() 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. #2: ![]() Title: A novel deamido-NAD+ binding site revealed by the trapped NAD-adenylate intermediate in the NAD+ synthetase structure Authors: Rizzi, M. / Bolognesi, M. / Coda, A. #3: ![]() Title: Crystal structure of NH3-dependent NAD+ synthetase from Bacillus subtilis Authors: Rizzi, M. / Nessi, C. / Mattevi, A. / Coda, A. / Bolognesi, M. / Galizzi, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 359 KB | Display | ![]() |
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PDB format | ![]() | 296 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 966.9 KB | Display | ![]() |
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Full document | ![]() | 981 KB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 47.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ee1S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a dimer from the asymmetric unit (chains A,B). |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30303.994 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: complexed with a reaction intermediate NAD-A, residue ADJ Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P08164, NAD+ synthase (glutamine-hydrolysing) |
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-Non-polymers , 5 types, 733 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ADJ.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ADJ.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 36 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: microgravity/vapor diffusion / pH: 8.5 Details: 25% PEG 400, 0.05M Tris, 0.05M MgCl2, 0.005M NaAD, 0.0025M ATP, pH 8.5, microgravity/vapor diffusion at 298K, microgravity/vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.2 / Method: vapor diffusion, hanging dropDetails: Devedjiev, Y., (2001) Acta Crystallogr., Sect.D, 57, 806. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.905 Å / Relative weight: 1 |
Reflection | Resolution: 1.028→30 Å / Num. all: 239033 / Num. obs: 231200 / % possible obs: 96.7 % / Observed criterion σ(I): -1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 32.8 |
Reflection shell | Resolution: 1.028→1.08 Å / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.4 / % possible all: 72.3 |
Reflection | *PLUS Highest resolution: 1.03 Å / % possible obs: 90 % / Num. measured all: 790765 |
Reflection shell | *PLUS Highest resolution: 1.03 Å / Lowest resolution: 1.1 Å / % possible obs: 75 % |
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Processing
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Refinement | Starting model: 1EE1 Resolution: 1.03→10 Å / Num. parameters: 47101 / Num. restraintsaints: 52229 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Luzzati coordinate error obs: 0.05 Å / Num. disordered residues: 18 / Occupancy sum hydrogen: 4272.09 / Occupancy sum non hydrogen: 5072.19 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.03→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.03→1.08 Å /
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 205215 / Rfactor obs: 0.118 / Rfactor Rfree: 0.1472 / Rfactor Rwork: 0.1163 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |