[English] 日本語
Yorodumi- PDB-5dwv: Crystal structure of the Luciferase complexed with substrate analogue -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dwv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Luciferase complexed with substrate analogue | ||||||
Components | Luciferin 4-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / luciferase / complex / substrate analogue / Photinus pyralis | ||||||
Function / homology | Function and homology information Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity / firefly luciferase / long-chain fatty acid-CoA ligase activity / fatty-acyl-CoA biosynthetic process / bioluminescence / peroxisome / protein-folding chaperone binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Photinus pyralis (common eastern firefly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Su, J. / Li, Z. / Yuan, Z. / Gu, L. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of the Luciferase complexed with substrate analogue Authors: Su, J. / Li, Z. / Yuan, Z. / Gu, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5dwv.cif.gz | 108 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5dwv.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 5dwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/5dwv ftp://data.pdbj.org/pub/pdb/validation_reports/dw/5dwv | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 63368.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photinus pyralis (common eastern firefly) Production host: Escherichia coli (E. coli) / References: UniProt: P08659, firefly luciferase |
---|---|
#2: Chemical | ChemComp-5J4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.52 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 / Details: Li2SO4, PEG8000, Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 2, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.43 Å / Num. obs: 165729 / % possible obs: 100 % / Redundancy: 7.3 % / Net I/σ(I): 26.48 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.3→29.43 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.51 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.43 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|