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Yorodumi- PDB-4mn0: Spatial structure of the novel light-sensitive photoprotein berov... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mn0 | |||||||||
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Title | Spatial structure of the novel light-sensitive photoprotein berovin from the ctenophore Beroe abyssicola in the Ca2+-loaded apoprotein conformation state | |||||||||
Components | Berovin | |||||||||
Keywords | LUMINESCENT PROTEIN / Ca2+-regulated photoprotein / Coelenterazine / Berovin / Bioluminescent protein / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG / EF-hand Ca2+-binding protein / Ca2+-regulated bioluminescent protein / Coelenterazine BindingCalcium Binding | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Beroe abyssicola (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | |||||||||
Authors | Liu, Z.J. / Stepanyuk, G.A. / Vysotski, E.S. / Lee, J. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG) | |||||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2013 Title: Spatial structure of the novel light-sensitive photoprotein berovin from the ctenophore Beroe abyssicola in the Ca(2+)-loaded apoprotein conformation state. Authors: Stepanyuk, G.A. / Liu, Z.J. / Burakova, L.P. / Lee, J. / Rose, J. / Vysotski, E.S. / 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 | 4mn0.cif.gz | 53.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mn0.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 4mn0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mn0_validation.pdf.gz | 427.9 KB | Display | wwPDB validaton report |
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Full document | 4mn0_full_validation.pdf.gz | 430.1 KB | Display | |
Data in XML | 4mn0_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 4mn0_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/4mn0 ftp://data.pdbj.org/pub/pdb/validation_reports/mn/4mn0 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25327.850 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Beroe abyssicola (invertebrata) / Gene: BA2, BA1, BA3, BA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H8ZZK1 | ||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: 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: 2.11 Å3/Da / Density % sol: 41.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (15 MG/ML) AND PRECIPITATE SOLUTION (0.2M MAGNESIUM NITRATE HEXAHYDRATE, 20% PEG 3350, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 94 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2006 |
Radiation | Monochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40.78 Å / Num. all: 13550 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique all: 833 / Rsym value: 0.41 / % possible all: 82.84 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→40.78 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.94 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.098 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40.78 Å
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