+Open data
-Basic information
Entry | Database: PDB / ID: 1sl8 | ||||||
---|---|---|---|---|---|---|---|
Title | Calcium-loaded apo-aequorin from Aequorea victoria | ||||||
Components | Aequorin 1 | ||||||
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 | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAS / Resolution: 1.7 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: Protein Sci. / Year: 2005 Title: All three Ca2+-binding loops of photoproteins bind calcium ions: The crystal structures of calcium-loaded apo-aequorin and apo-obelin. Authors: Deng, L. / Vysotski, E.S. / Markova, S.V. / 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 |
| ||||||
Remark 999 | SEQUENCE Authors informed that there are several isoforms of this protein from the same species. ...SEQUENCE Authors informed that there are several isoforms of this protein from the same species. The conflict at residue 138 arises because their sequence is one of the isoforms. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1sl8.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1sl8.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 1sl8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sl8_validation.pdf.gz | 415.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1sl8_full_validation.pdf.gz | 416.3 KB | Display | |
Data in XML | 1sl8_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 1sl8_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/1sl8 ftp://data.pdbj.org/pub/pdb/validation_reports/sl/1sl8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21888.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: pET19b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: P07164 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.07 % |
---|---|
Crystal grow | Temperature: 277 K / Method: modified microbatch / pH: 4.6 Details: 30% v/v 2-methyl-2,4-pentanediol, 0.1M sodium acetate, pH 4.6, modified microbatch, temperature 277K |
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||
Detector |
| ||||||||||||||||||
Radiation | Monochromator: Confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||
Reflection | Resolution: 1.7→50 Å / Num. obs: 22954 / % possible obs: 98.8 % / Redundancy: 8.3 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.38 / Net I/σ(I): 45.9 | ||||||||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.7 / % possible all: 91.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAS / Resolution: 1.7→50.64 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.588 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.112 / 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: 30.473 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→50.64 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.743 Å / Total num. of bins used: 20 /
|