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Yorodumi- PDB-4m46: Crystal structure of a green-emitter native of Lampyris turkestan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m46 | ||||||
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Title | Crystal structure of a green-emitter native of Lampyris turkestanicus luciferase | ||||||
Components | Luciferase | ||||||
Keywords | OXIDOREDUCTASE / Bioluminescence / Oxidoreductase activity / monooxygenase / ATP binding / Luciferin-binding / light emitting | ||||||
Function / homology | Function and homology information Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity / firefly luciferase / bioluminescence / peroxisome Similarity search - Function | ||||||
Biological species | Lampyris turkestanicus (Iranian firefly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Sharafian, Z. / Hosseinkhani, S. / Naderi-manesh, H. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2013 Title: Crystal structure of native and a mutant of Lampyris turkestanicus luciferase implicate in bioluminescence color shift. Authors: Kheirabadi, M. / Sharafian, Z. / Naderi-Manesh, H. / Heineman, U. / Gohlke, U. / Hosseinkhani, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m46.cif.gz | 103.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m46.ent.gz | 76.7 KB | Display | PDB format |
PDBx/mmJSON format | 4m46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/4m46 ftp://data.pdbj.org/pub/pdb/validation_reports/m4/4m46 | HTTPS FTP |
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-Related structure data
Related structure data | 3qyaC 1lciS C: citing same article (ref.) S: Starting model for refinement |
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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: 64114.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lampyris turkestanicus (Iranian firefly) Strain: Lampyris / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5UFR2, firefly luciferase |
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#2: Water | ChemComp-HOH / |
Sequence details | ACCORDING TO THE AUTHORS THE ELECTRON DENSITY FOR RESIDUE 268 IS UNAMBIGUOUS, AND IT CLEARLY SHOWS ...ACCORDING TO THE AUTHORS THE ELECTRON DENSITY FOR RESIDUE 268 IS UNAMBIGUOU |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.92 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM MES Sodium salt, 40% v/v PEG 400, 5% w/v PEG 3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9778 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2011 / Details: Dynamically bendable mirror |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→96.63 Å / Num. all: 19048 / Num. obs: 18984 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.167 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LCI Resolution: 2.7→96.63 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.858 / SU B: 10.71 / SU ML: 0.222 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.589 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.119 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→96.63 Å
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Refine LS restraints |
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