[English] 日本語
Yorodumi- PDB-2d1q: Crystal structure of the thermostable Japanese Firefly Luciferase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d1q | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the thermostable Japanese Firefly Luciferase complexed with MgATP | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2d1q.cif.gz | 117.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2d1q.ent.gz | 87.5 KB | Display | PDB format |
PDBx/mmJSON format | 2d1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/2d1q ftp://data.pdbj.org/pub/pdb/validation_reports/d1/2d1q | HTTPS FTP |
---|
-Related structure data
Related structure data | 2d1rC 2d1sC 2d1tC 1lciS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Chemical | ChemComp-AMP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.2 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: PEG4000, Lithium chrolide, ATP, magnesium chloride, Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 16, 1999 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→60 Å / Num. all: 25394 / Num. obs: 25394 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.55 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4 / Num. unique all: 2304 / % possible all: 91.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LCI Resolution: 2.3→60 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.834 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.319 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 22.972 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→60 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20 /
|