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Yorodumi- PDB-1jf2: Crystal Structure of W92F obelin mutant from Obelia longissima at... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jf2 | ||||||
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Title | Crystal Structure of W92F obelin mutant from Obelia longissima at 1.72 Angstrom resolution | ||||||
Components | obelin | ||||||
Keywords | LUMINESCENT PROTEIN / bioluminescence / calcium-regulated photoprotein / obelin / obelia / hydroid | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Obelia longissima (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Liu, Z.-J. / Vysotski, E.S. / Deng, L. / Markova, S.V. / Lee, J. / Rose, J.P. / Wang, B.-C. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Violet bioluminescence and fast kinetics from W92F obelin: structure-based proposals for the bioluminescence triggering and the identification of the emitting species. Authors: Vysotski, E.S. / Liu, Z.J. / Markova, S.V. / Blinks, J.R. / Deng, L. / Frank, L.A. / Herko, M. / Malikova, N.P. / Rose, J.P. / Wang, B.C. / Lee, J. #1: Journal: Protein Sci. / Year: 2000 Title: Structure of the Ca2+-regulated photoprotein obelin at 1.7 A resolution determined directly from its sulfur substructure. Authors: Liu, Z.J. / Vysotski, E.S. / Chen, C.J. / Rose, J.P. / Lee, J. / Wang, B.C. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Preparation and preliminary study of crystals of the recombinant calcium-regulated photoprotein obelin from the bioluminescent hydroid Obelia longissima. Authors: Vysotski, E.S. / Liu, Z.J. / Rose, J. / Wang, B.C. / Lee, J. #3: Journal: Bioluminescence and Chemiluminescence 2000 / Year: 2001 Title: Obelin crystal structure: implications for the bioluminescence mechanism Authors: Vysotski, E. / Liu, Z.-J. / Deng, L. / Rose, J. / Wang, B.-C. / Lee, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jf2.cif.gz | 55.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jf2.ent.gz | 39.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/1jf2 ftp://data.pdbj.org/pub/pdb/validation_reports/jf/1jf2 | HTTPS FTP |
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-Related structure data
Related structure data | 1el4S 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: 22215.869 Da / Num. of mol.: 1 / Mutation: W92F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Obelia longissima (invertebrata) / Plasmid: pOL-92F / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold / References: UniProt: Q27709 |
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#2: Chemical | ChemComp-CZH / |
#3: 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: 2.32 Å3/Da / Density % sol: 47.04 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 8000, potassium phosphate, hexaminecobaltic chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Details: Deng, L., (2001) FEBS Lett., 506, 281. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 8, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 23136 / Num. obs: 21633 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.3 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 18.08 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.35 / % possible all: 87.7 |
Reflection | *PLUS % possible obs: 99.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS Rmerge(I) obs: 0.08 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EL4 Resolution: 1.72→26.28 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 259784.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.47 Å2 / ksol: 0.4095 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.72→26.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.83 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 7.9 % | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.359 / % reflection Rfree: 8 % / Rfactor Rwork: 0.294 |