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Yorodumi- PDB-1s36: Crystal structure of a Ca2+-discharged photoprotein: Implications... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s36 | ||||||
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Title | Crystal structure of a Ca2+-discharged photoprotein: Implications for the mechanisms of the calcium trigger and the bioluminescence | ||||||
Components | Obelin | ||||||
Keywords | LUMINESCENT PROTEIN / Photoprotein / obelin / bioluminescence / calcium binding / EF-hand / aequorin / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Obelia longissima (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Deng, L. / Markova, S.V. / Vysotski, E.S. / Liu, Z.-J. / Lee, J. / Rose, J. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal structure of a Ca2+-discharged photoprotein: implications for mechanisms of the calcium trigger and bioluminescence Authors: Deng, L. / Markova, S.V. / Vysotski, E.S. / Liu, Z.-J. / 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.S. / 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.S. / 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.S. / Liu, Z.-J. / Markova, S.V. / Malikova, N.P. / 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.S. / Liu, Z.-J. / Markova, S.V. / Blinks, J. / Deng, L. / Frank, L.A. / Herko, M. / Malikova, N.P. / Rose, J.P. / Wang, B.-C. / Lee, J. #5: 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. #6: Journal: To be Published Title: Preparation and X-ray Crystallographic Analysis of the Ca2+-discharged Photoprotein Obelin Authors: Deng, L. / Markova, S.V. / Vysotski, E.S. / Liu, Z.-J. / Lee, J. / Rose, J. / Wang, B.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s36.cif.gz | 57.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s36.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 1s36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s36_validation.pdf.gz | 452.4 KB | Display | wwPDB validaton report |
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Full document | 1s36_full_validation.pdf.gz | 452.3 KB | Display | |
Data in XML | 1s36_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 1s36_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/1s36 ftp://data.pdbj.org/pub/pdb/validation_reports/s3/1s36 | HTTPS FTP |
-Related structure data
Related structure data | 1jf2S 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
-Protein , 1 types, 1 molecules A
#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: pET19b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q27709 |
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-Non-polymers , 5 types, 149 molecules
#2: Chemical | ChemComp-NA / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-CEI / |
#5: Chemical | ChemComp-GOL / |
#6: 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: 2.31 Å3/Da / Density % sol: 46.86 % |
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Crystal grow | Temperature: 277 K / Method: modified microbatch / pH: 7.5 Details: 1.5 M tri-sodium citrate, 0.1 M Na-HEPES, pH 7.5, modified microbatch, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Nov 20, 2002 / Details: Rigaku/msc HiRes2 |
Radiation | Monochromator: Confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→72.46 Å / Num. obs: 15775 / % possible obs: 1 % / Observed criterion σ(I): -3 / Redundancy: 14.91 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.06 / Net I/σ(I): 9.37 |
Reflection shell | Resolution: 1.96→2.05 Å / Mean I/σ(I) obs: 2.11 / Num. unique all: 1982 / Rsym value: 0.19 / % possible all: 0.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JF2 Resolution: 1.96→50 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.886 / SU B: 3.274 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.174 / 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: 16.388 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.957→2.008 Å / Total num. of bins used: 20
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