[English] 日本語
![](img/lk-miru.gif)
- PDB-1kkb: Complex of Escherichia coli Adenylosuccinate Synthetase with IMP ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1kkb | ||||||
---|---|---|---|---|---|---|---|
Title | Complex of Escherichia coli Adenylosuccinate Synthetase with IMP and Hadacidin | ||||||
![]() | Adenylosuccinate Synthetase | ||||||
![]() | LIGASE / GTP-HYDROLYSING ENZYMES / PURINE NUCLEOTIDE / BIOSYNTHESIS / INDUCED FIT | ||||||
Function / homology | ![]() adenylosuccinate synthase / adenylosuccinate synthase activity / adenosine biosynthetic process / IMP metabolic process / 'de novo' AMP biosynthetic process / nucleobase-containing small molecule interconversion / purine nucleotide biosynthetic process / guanosine tetraphosphate binding / DNA damage response / GTP binding ...adenylosuccinate synthase / adenylosuccinate synthase activity / adenosine biosynthetic process / IMP metabolic process / 'de novo' AMP biosynthetic process / nucleobase-containing small molecule interconversion / purine nucleotide biosynthetic process / guanosine tetraphosphate binding / DNA damage response / GTP binding / magnesium ion binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hou, Z. / Wang, W. / Fromm, H.J. / Honzatko, R.B. | ||||||
![]() | ![]() Title: IMP Alone Organizes the Active Site of Adenylosuccinate Synthetase from Escherichia coli. Authors: Hou, Z. / Wang, W. / Fromm, H.J. / Honzatko, R.B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 102.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 77.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 755.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 768.4 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The asymmetry unit is one subunit. The functional synthetase is a dimer |
-
Components
#1: Protein | Mass: 47400.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P12283, UniProt: P0A7D4*PLUS, adenylosuccinate synthase |
---|---|
#2: Chemical | ChemComp-HDA / |
#3: Chemical | ChemComp-IMP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.33 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, HEPES, IMP, Hadacidin, magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1998 / Details: Graphite monochromator |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 22708 / Num. obs: 22708 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rsym value: 0.122 |
Reflection shell | Resolution: 2.6→2.9 Å / % possible all: 90 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 91 % / Num. measured all: 121026 / Rmerge(I) obs: 0.12 |
Reflection shell | *PLUS % possible obs: 90 % |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→5 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 5 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.18 / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.18 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|