+Open data
-Basic information
Entry | Database: PDB / ID: 5dv9 | ||||||
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Title | Crystal structure of the Luciferase | ||||||
Components | Luciferin 4-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / luciferase / apo / 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: 2.4 Å | ||||||
Authors | Su, J. / Li, Z. / Yuan, Z. / Gu, L. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of the Luciferase Authors: Su, J. / Li, Z. / Yuan, Z. / Gu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dv9.cif.gz | 123.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dv9.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 5dv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/5dv9 ftp://data.pdbj.org/pub/pdb/validation_reports/dv/5dv9 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 / Details: Li2SO4, PEG 8000, Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→41.71 Å / Num. obs: 363262 / % possible obs: 100 % / Redundancy: 13.5 % / Net I/σ(I): 32.13 |
-Processing
Software |
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Refinement | Resolution: 2.4→41.708 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→41.708 Å
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Refine LS restraints |
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LS refinement shell |
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