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Yorodumi- PDB-4b30: Structure of the mutant V44A of the fluorescent protein KillerRed -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b30 | |||||||||
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Title | Structure of the mutant V44A of the fluorescent protein KillerRed | |||||||||
Components | (KILLERRED) x 2 | |||||||||
Keywords | FLUORESCENT PROTEIN / PHOTOBLEACHING / PHOTOCONVERSION / ROS | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | ANTHOMEDUSAE SP. DC-2005 (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Carpentier, P. / de Rosny, E. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2012 Title: Gfp-Like Phototransformation Mechanisms in the Cytotoxic Fluorescent Protein Killerred Unraveled by Structural and Spectroscopic Investigations. Authors: De Rosny, E. / Carpentier, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b30.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b30.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 4b30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b30_validation.pdf.gz | 447.7 KB | Display | wwPDB validaton report |
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Full document | 4b30_full_validation.pdf.gz | 460.4 KB | Display | |
Data in XML | 4b30_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 4b30_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/4b30 ftp://data.pdbj.org/pub/pdb/validation_reports/b3/4b30 | HTTPS FTP |
-Related structure data
Related structure data | 2wiqS S: Starting model for refinement |
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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 , 2 types, 2 molecules AB
#1: Protein | Mass: 26417.662 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ANTHOMEDUSAE SP. DC-2005 (invertebrata) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q2TCH5 |
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#2: Protein | Mass: 26401.662 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ANTHOMEDUSAE SP. DC-2005 (invertebrata) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q2TCH5 |
-Non-polymers , 5 types, 277 molecules
#3: Chemical | ChemComp-SO4 / | ||||||
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#4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.96 Å3/Da / Density % sol: 69 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: HANGING DROP VAPOR DIFFUSION, A44-KR (15 MG/ML), 1.8 M MGSO4, 100 MM BICINE PH 8, 2% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 5, 2010 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 45765 / % possible obs: 99.6 % / Observed criterion σ(I): 4.5 / Redundancy: 11 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 4.5 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WIQ Resolution: 2.1→116.32 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.216 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 39.432 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→116.32 Å
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Refine LS restraints |
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