[English] 日本語
Yorodumi- PDB-1rl9: Crystal structure of Creatine-ADP arginine kinase ternary complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rl9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Creatine-ADP arginine kinase ternary complex | ||||||
Components | Arginine kinase | ||||||
Keywords | TRANSFERASE / arginine kinase | ||||||
Function / homology | Function and homology information arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / phosphorylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Limulus polyphemus (Atlantic horseshoe crab) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Azzi, A. / Clark, S.A. / Ellington, R.W. / Chapman, M.S. | ||||||
Citation | Journal: Protein Sci. / Year: 2004 Title: The role of phosphagen specificity loops in arginine kinase. Authors: Azzi, A. / Clark, S.A. / Ellington, W.R. / Chapman, M.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1rl9.cif.gz | 95.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1rl9.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 1rl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/1rl9 ftp://data.pdbj.org/pub/pdb/validation_reports/rl/1rl9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1bgoS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40308.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Limulus polyphemus (Atlantic horseshoe crab) Plasmid: PET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P51541, arginine kinase |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-IOM / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.76 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 6000, magnesium chloride, ATP, Creatine, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 24, 2002 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 57917 / % possible obs: 89.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 13 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.101 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.45→1.5 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.445 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BGO Resolution: 1.45→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Displacement parameters | Biso mean: 15.6 Å2 | ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→10 Å
|