[English] 日本語
![](img/lk-miru.gif)
- PDB-1yum: Crystal Structure of Nicotinic Acid Mononucleotide Adenylyltransf... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1yum | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Nicotinic Acid Mononucleotide Adenylyltransferase from Pseudomonas aeruginosa | ||||||
![]() | 'Probable nicotinate-nucleotide adenylyltransferase | ||||||
![]() | TRANSFERASE / alpha/beta domain | ||||||
Function / homology | ![]() nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yoon, H.J. / Kim, H.L. / Mikami, B. / Suh, S.W. | ||||||
![]() | ![]() Title: Crystal structure of nicotinic acid mononucleotide adenylyltransferase from Pseudomonas aeruginosa in its Apo and substrate-complexed forms reveals a fully open conformation Authors: Yoon, H.J. / Kim, H.L. / Mikami, B. / Suh, S.W. | ||||||
History |
| ||||||
Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAINS. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAINS. THE BIOLOGICAL UNIT IS NOT ASSIGNED. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 204.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 161.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 52.1 KB | Display | |
Data in CIF | ![]() | 71.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer generated from the tetramer in the asymmetric unit by the operations: -x, 1/2+y, -z |
-
Components
#1: Protein | ' Mass: 27074.783 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9HX21, nicotinate-nucleotide adenylyltransferase #2: Chemical | ChemComp-CIT / #3: Chemical | ChemComp-NCN / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.7 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: bis-tris propane, trisodium citrate, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2004 / Details: mirrors |
Radiation | Monochromator: quasi-monochromatic X-ray / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.85 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 118067 / Num. obs: 118041 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 21.74 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3 % / Rmerge(I) obs: 0.266 / Num. unique all: 12046 / % possible all: 98.9 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: apo NaMN AT Resolution: 1.7→10 Å / Num. parameters: 31002 / Num. restraintsaints: 29215 / Cross valid method: THROUGHOUT / σ(I): 0 Details: THIS IS A TWINNED STRUCTURE. THE TWINNING OPERATOR IS (H,K,L) -> (H,-K,-L) AND THE TWINNING FRACTION IS 0.49421
| |||||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 26 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7590.14 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|