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Yorodumi- PDB-2vzx: Structural and spectroscopic characterization of photoconverting ... -
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-Basic information
Entry | Database: PDB / ID: 2vzx | ||||||||||||
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Title | Structural and spectroscopic characterization of photoconverting fluorescent protein Dendra2 | ||||||||||||
Components | Green fluorescent protein | ||||||||||||
Keywords | FLUORESCENT PROTEIN / PHOTOACTIVATION / GFP-LIKE PROTEIN / DENDRA2 | ||||||||||||
Function / homology | Function and homology information bioluminescence / generation of precursor metabolites and energy / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Dendronephthya sp. SSAL-2002 (invertebrata) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Adam, V. / Nienhaus, K. / Bourgeois, D. / Nienhaus, G.U. | ||||||||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structural Basis of Enhanced Photoconversion Yield in Green Fluorescent Protein-Like Protein Dendra2. Authors: Adam, V. / Nienhaus, K. / Bourgeois, D. / Nienhaus, G.U. | ||||||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vzx.cif.gz | 387.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vzx.ent.gz | 317.9 KB | Display | PDB format |
PDBx/mmJSON format | 2vzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vzx_validation.pdf.gz | 523.8 KB | Display | wwPDB validaton report |
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Full document | 2vzx_full_validation.pdf.gz | 558.4 KB | Display | |
Data in XML | 2vzx_validation.xml.gz | 83.3 KB | Display | |
Data in CIF | 2vzx_validation.cif.gz | 112.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/2vzx ftp://data.pdbj.org/pub/pdb/validation_reports/vz/2vzx | HTTPS FTP |
-Related structure data
Related structure data | 1zuxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26485.045 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dendronephthya sp. SSAL-2002 (invertebrata) Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15PREP4 / References: UniProt: Q8T6U0 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | pH: 8.8 / Details: 32% PEG 3350, 0.1M MAGNESIUM NITRATE, PH 8.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 |
Detector | Type: ADSC CCD / Detector: CCD / Details: TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 2→33.5 Å / Num. obs: 113215 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 1.95 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.15 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 1.85 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.42 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZUX Resolution: 2→33.5 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.885 / SU B: 5.371 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.21 / 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: 21.816 Å2
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Refinement step | Cycle: LAST / Resolution: 2→33.5 Å
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