+Open data
-Basic information
Entry | Database: PDB / ID: 7eg2 | ||||||
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Title | Crystal structure of the apoAequorin complex with (S)-daCTZ | ||||||
Components | Aequorin-2 | ||||||
Keywords | OXIDOREDUCTASE / Aequorin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å | ||||||
Authors | Tomabechi, Y. / Shirouzu, M. | ||||||
Citation | Journal: Plos One / Year: 2021 Title: Chiral deaza-coelenterazine analogs for probing a substrate-binding site in the Ca2+-binding photoprotein aequorin. Authors: Inouye, S. / Sumida, Y. / Tomabechi, Y. / Taguchi, J. / Shirouzu, M. / Hosoya, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eg2.cif.gz | 636.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eg2.ent.gz | 530.7 KB | Display | PDB format |
PDBx/mmJSON format | 7eg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eg2_validation.pdf.gz | 4.6 MB | Display | wwPDB validaton report |
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Full document | 7eg2_full_validation.pdf.gz | 4.6 MB | Display | |
Data in XML | 7eg2_validation.xml.gz | 122.2 KB | Display | |
Data in CIF | 7eg2_validation.cif.gz | 163.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/7eg2 ftp://data.pdbj.org/pub/pdb/validation_reports/eg/7eg2 | HTTPS FTP |
-Related structure data
Related structure data | 7eg3C 1ej3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 22544.117 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli) / References: UniProt: P02592 #2: Chemical | ChemComp-J2X / ( #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.76 Å3/Da / Density % sol: 55.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Jun 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→50 Å / Num. obs: 183193 / % possible obs: 95.5 % / Redundancy: 1.99 % / CC1/2: 0.75 / Net I/σ(I): 7.75 |
Reflection shell | Resolution: 2.22→2.36 Å / Num. unique obs: 27998 / CC1/2: 0.1 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ej3 Resolution: 2.22→41.64 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 28.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.33 Å2 / Biso mean: 34.0557 Å2 / Biso min: 13.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.22→41.64 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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