[English] 日本語
![](img/lk-miru.gif)
- PDB-1k4m: Crystal structure of E.coli nicotinic acid mononucleotide adenyly... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1k4m | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of E.coli nicotinic acid mononucleotide adenylyltransferase complexed to deamido-NAD | ||||||
![]() | NaMN adenylyltransferase | ||||||
![]() | TRANSFERASE / Nucleotidyltransferase | ||||||
Function / homology | ![]() NAD salvage / 'de novo' NAD biosynthetic process from aspartate / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhang, H. / Zhou, T. / Kurnasov, O. / Cheek, S. / Grishin, N.V. / Osterman, A. | ||||||
![]() | ![]() Title: Crystal structures of E. coli nicotinate mononucleotide adenylyltransferase and its complex with deamido-NAD. Authors: Zhang, H. / Zhou, T. / Kurnasov, O. / Cheek, S. / Grishin, N.V. / Osterman, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 151.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 121 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 616.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 641.3 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 28.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k4kSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological unit of the protein is monomer |
-
Components
#1: Protein | Mass: 24553.871 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A752, nicotinate-nucleotide adenylyltransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.06 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Na citrate, NaCl, Tris, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 5, 2001 / Details: Osmic mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 59943 / Num. obs: 57802 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. measured all: 180068 / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 67.5 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 1.8 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1k4k Resolution: 1.9→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
| ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor obs: 0.206 / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.206 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|