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Yorodumi- PDB-2d1r: Crystal structure of the thermostable Japanese firefly Luciferase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d1r | ||||||
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Title | Crystal structure of the thermostable Japanese firefly Luciferase complexed with OXYLUCIFERIN and AMP | ||||||
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 / bioluminescence / peroxisome / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Luciola cruciata (Japanese firefly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 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 | 2d1r.cif.gz | 132.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d1r.ent.gz | 99 KB | Display | PDB format |
PDBx/mmJSON format | 2d1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/2d1r ftp://data.pdbj.org/pub/pdb/validation_reports/d1/2d1r | HTTPS FTP |
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-Related structure data
Related structure data | 2d1qSC 2d1sC 2d1tC 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: 60133.156 Da / Num. of mol.: 1 / Mutation: T217I 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 | ChemComp-AMP / |
#3: Chemical | ChemComp-OLU / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: PEG4000, Lithium chrolide, Magnesium chloride, ATP, D-Luciferin, Teis-HCl, pH 8.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 29, 2001 |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→55 Å / Num. all: 73719 / Num. obs: 73719 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3 / Num. unique all: 7056 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2D1Q Resolution: 1.6→55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.469 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.09 / 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: 16.437 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20 /
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