[English] 日本語
![](img/lk-miru.gif)
- PDB-4bhl: Crystal structure of Litopenaeus vannamei arginine kinase in bina... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4bhl | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Litopenaeus vannamei arginine kinase in binary complex with arginine | ||||||
![]() | ARGININE KINASE | ||||||
![]() | TRANSFERASE / BINARY COMPLEX / PHOSPHAGEN | ||||||
Function / homology | ![]() dTDP metabolic process / arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / arginine binding / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lopez-Zavala, A.A. / Garcia-Orozco, K.D. / Carrasco-Miranda, J.S. / Hernandez-Flores, J.M. / Sugich-Miranda, R. / Velazquez-Contreras, E.F. / Criscitiello, M.F. / Brieba, L.G. / Rudino-Pinera, E. / Sotelo-Mundo, R.R. | ||||||
![]() | ![]() Title: Crystal Structure of Shrimp Arginine Kinase in Binary Complex with Arginine-A Molecular View of the Phosphagen Precursor Binding to the Enzyme. Authors: Lopez-Zavala, A.A. / Garcia-Orozco, K.D. / Carrasco-Miranda, J.S. / Sugich-Miranda, R. / Velazquez-Contreras, E.F. / Criscitiello, M.F. / Brieba, L.G. / Rudino-Pinera, E. / Sotelo-Mundo, R.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 88.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 64.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4bg4C ![]() 4am1S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 40207.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Tissue: TAIL MUSCLE / References: UniProt: Q004B5, arginine kinase |
---|---|
#2: Chemical | ChemComp-ARG / |
#3: Chemical | ChemComp-BME / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | BETA-MERCAPTOETHANOL (BME): BETA-MERCAPTOETHANOL IS COVALENTLY BOUNDED TO CYS 139. ARGININE (ARG): ...BETA-MERCAPTOET |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.5 % / Description: NONE |
---|---|
Crystal grow | Method: microbatch / pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED FROM 0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5 AND 30 % (W/V) PEG 8000 USING THE MICROBATCH METHOD |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 5, 2012 Details: 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING |
Radiation | Monochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→19.1 Å / Num. obs: 26516 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 7.1 % / Biso Wilson estimate: 14.29 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.4 / % possible all: 96.1 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4AM1 Resolution: 1.9→46.461 Å / SU ML: 0.2 / σ(F): 1.97 / Phase error: 18.62 / Stereochemistry target values: ML Details: RESIDUES 312-319 ARE DISORDERED AND WERE NOT INCLUDED IN THE FINAL MODEL.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.96 Å2 / ksol: 0.412 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.3 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→46.461 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|