+Open data
-Basic information
Entry | Database: PDB / ID: 1qv0 | ||||||
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Title | Atomic resolution structure of obelin from Obelia longissima | ||||||
Components | Obelin | ||||||
Keywords | LUMINESCENT PROTEIN / Photoprotein / obelin / bioluminescence / atomic resolution / calcium binding / EF-hand | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Obelia longissima (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Liu, Z.J. / Vysotski, E.S. / Deng, L. / Lee, J. / Rose, J. / Wang, B.C. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2003 Title: Atomic resolution structure of obelin: soaking with calcium enhances electron density of the second oxygen atom substituted at the C2-position of coelenterazine. Authors: Liu, Z.J. / Vysotski, E.S. / Deng, L. / Lee, J. / Rose, J. / Wang, B.C. #1: Journal: Protein Sci. / Year: 2000 Title: Structure of the Ca2+-regulated photoprotein obelin at 1.7 resolution determined directly from its sulfur substructure Authors: Liu, Z.-J. / Vysotski, E. / Chen, C.-J. / Rose, J. / 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. / Liu, Z.-J. / Rose, J. / Wang, B.-C. / Lee, J. #3: Journal: FEBS Lett. / Year: 2001 Title: Structural basis for the emission of violet bioluminescence from a W92F obelin mutant Authors: Deng, L. / Vysotski, E. / Liu, Z.-J. / Markova, S. / Malikova, N. / Lee, J. / Rose, J. / Wang, B.-C. #4: 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. / Liu, Z.-J. / Markova, S. / Blinks, J. / Deng, L. / Frank, L. / Herko, M. / Malikova, N. / 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 | 1qv0.cif.gz | 97.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qv0.ent.gz | 71.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/1qv0 ftp://data.pdbj.org/pub/pdb/validation_reports/qv/1qv0 | HTTPS FTP |
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-Related structure data
Related structure data | 1qv1C 1el4S S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22238.904 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Obelia longissima (invertebrata) / Plasmid: pET19-OL8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold / References: UniProt: Q27709, Renilla-type luciferase |
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-Non-polymers , 5 types, 238 molecules
#2: Chemical | #3: Chemical | ChemComp-K / | #4: Chemical | ChemComp-CZH / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 50 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG8000, potassium phosphate, hexaminecobaltic chloride , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion, hanging dropDetails: Vysotski, E.S., (2001) Acta Crystallogr., D57, 1919. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 12, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. all: 86186 / Num. obs: 85842 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.046 |
Reflection shell | Resolution: 1.1→1.16 Å / Rmerge(I) obs: 0.096 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EL4 Resolution: 1.1→10 Å / Num. parameters: 15166 / Num. restraintsaints: 18501 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.0153
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Displacement parameters | Biso mean: 10.468 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 9 / Occupancy sum hydrogen: 1382 / Occupancy sum non hydrogen: 1783.07 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.1 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.161 / Rfactor Rwork: 0.15 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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