[English] 日本語
![](img/lk-miru.gif)
- PDB-1lon: Crystal Structure of the Recombinant Mouse-Muscle Adenylosuccinat... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1lon | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Recombinant Mouse-Muscle Adenylosuccinate Synthetase Complexed with 6-phosphoryl-IMP, GDP and Hadacidin | ||||||
![]() | adenylosuccinate synthetase | ||||||
![]() | LIGASE / Purine biosynthesis / GTP-binding | ||||||
Function / homology | ![]() Purine ribonucleoside monophosphate biosynthesis / purine nucleotide metabolic process / adenylosuccinate synthase / adenylosuccinate synthase activity / aspartate metabolic process / IMP metabolic process / 'de novo' AMP biosynthetic process / AMP salvage / actin filament binding / GTPase activity ...Purine ribonucleoside monophosphate biosynthesis / purine nucleotide metabolic process / adenylosuccinate synthase / adenylosuccinate synthase activity / aspartate metabolic process / IMP metabolic process / 'de novo' AMP biosynthetic process / AMP salvage / actin filament binding / GTPase activity / GTP binding / magnesium ion binding / identical protein binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Iancu, C.V. / Borza, T. / Fromm, H.J. / Honzatko, R.B. | ||||||
![]() | ![]() Title: IMP, GTP, and 6-phosphoryl-IMP complexes of recombinant mouse muscle adenylosuccinate synthetase. Authors: Iancu, C.V. / Borza, T. / Fromm, H.J. / Honzatko, R.B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 105.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 78.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 28.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1iweC ![]() 1lnyC ![]() 1looC ![]() 1j4bS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer. The asymmetric unit contains one monomer. The other monomer is generated by the symmetry operation: -y, -x, 1/2-z. |
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 50321.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 190 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/IMO.gif)
![](data/chem/img/HDA.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IMO.gif)
![](data/chem/img/HDA.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / |
---|---|
#3: Chemical | ChemComp-IMO / |
#4: Chemical | ChemComp-HDA / |
#5: Chemical | ChemComp-GDP / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.46 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8000, magnesium acetate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-2 / Detector: CCD / Date: Apr 20, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 32291 / Num. obs: 31207 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.3 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 37.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 8 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 4.6 / Num. unique all: 3350 / % possible all: 90 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 32291 / % possible obs: 98.5 % / Num. measured all: 266913 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS Lowest resolution: 2.2 Å / % possible obs: 99.5 % / Rmerge(I) obs: 0.178 |
-
Processing
Software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1J4B Resolution: 2.1→10 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||
Displacement parameters | Biso mean: 40.7 Å2
| |||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
| |||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015
| |||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.224 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.315 / Rfactor Rwork: 0.313 |