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Yorodumi- PDB-2d1t: Crystal structure of the thermostable Japanese Firefly Luciferase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d1t | ||||||
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Title | Crystal structure of the thermostable Japanese Firefly Luciferase red-color emission S286N mutant complexed with High-energy intermediate analogue | ||||||
Components | Luciferin 4-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / ALPHA/BETA / BETA BARREL / ALPHA+BETA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
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 / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Luciola cruciata (Japanese firefly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å | ||||||
Authors | Nakatsu, T. / Ichiyama, S. / Hiratake, J. / Saldanha, A. / Kobashi, N. / Sakata, K. / Kato, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Nature / Year: 2006 Title: Structural basis for the spectral difference in luciferase bioluminescence. Authors: Nakatsu, T. / Ichiyama, S. / Hiratake, J. / Saldanha, A. / Kobashi, N. / Sakata, K. / Kato, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d1t.cif.gz | 137.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d1t.ent.gz | 102.9 KB | Display | PDB format |
PDBx/mmJSON format | 2d1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d1t_validation.pdf.gz | 739.6 KB | Display | wwPDB validaton report |
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Full document | 2d1t_full_validation.pdf.gz | 742.1 KB | Display | |
Data in XML | 2d1t_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 2d1t_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/2d1t ftp://data.pdbj.org/pub/pdb/validation_reports/d1/2d1t | HTTPS FTP |
-Related structure data
Related structure data | 2d1qC 2d1rC 2d1sSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 60160.172 Da / Num. of mol.: 1 / Mutation: T217I,S286N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Luciola cruciata (Japanese firefly) / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P13129, firefly luciferase | ||||
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#2: Chemical | #3: Chemical | ChemComp-SLU / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.8 Details: PEG4000, Lithium chrolide, Magnesium chloride, HEPES, 5'-O-[N-(dehydroluciferyl)-sulfamoyl] adenosine, pH 7.8, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 15, 2002 |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→25 Å / Num. all: 94838 / Num. obs: 94838 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Rsym value: 0.09 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 13298 / Rsym value: 0.283 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2D1S Resolution: 1.45→25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.922 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.451→1.488 Å / Total num. of bins used: 20 /
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