+Open data
-Basic information
Entry | Database: PDB / ID: 2v4e | ||||||
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Title | A non-cytotoxic DsRed variant for whole-cell labeling | ||||||
Components | (RED FLUORESCENT PROTEIN DRFP583) x 3 | ||||||
Keywords | FLUORESCENT PROTEIN / DSRED / CHROMOPHORE / LUMINESCENCE / PHOTOPROTEIN | ||||||
Function / homology | Green Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta Function and homology information | ||||||
Biological species | DISCOSOMA SP. (sea anemone) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Strack, R.L. / Strongin, D.E. / Bhattacharyya, D. / Tao, W. / Berman, A. / Broxmeyer, H.E. / Keenan, R.J. / Glick, B.S. | ||||||
Citation | Journal: Nat.Methods / Year: 2008 Title: A Noncytotoxic Dsred Variant for Whole-Cell Labeling. Authors: Strack, R.L. / Strongin, D.E. / Bhattacharyya, D. / Tao, W. / Berman, A. / Broxmeyer, H.E. / Keenan, R.J. / Glick, B.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v4e.cif.gz | 355.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v4e.ent.gz | 292.4 KB | Display | PDB format |
PDBx/mmJSON format | 2v4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/2v4e ftp://data.pdbj.org/pub/pdb/validation_reports/v4/2v4e | HTTPS FTP |
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-Related structure data
Related structure data | 2vaeS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25179.713 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THIS IS AN ENGINEERED VARIANT OF DSRED / Source: (gene. exp.) DISCOSOMA SP. (sea anemone) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH10B | ||
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#2: Protein | Mass: 25176.689 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THIS IS AN ENGINEERED VARIANT OF DSRED / Source: (gene. exp.) DISCOSOMA SP. (sea anemone) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH10B | ||
#3: Protein | Mass: 25178.662 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: THIS IS AN ENGINEERED VARIANT OF DSRED / Source: (gene. exp.) DISCOSOMA SP. (sea anemone) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH10B #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: 2.84 Å3/Da / Density % sol: 58 % / Description: DIFFRACITON IS ANIOSTROPIC |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 100 MM BIS-TRIS, PH 5.5 200 MM AMMONIUM SULFATE, 16% PEG8000, VAPOR DIFFUSION, SITTING DROP, 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 92897 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / % possible all: 84.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VAE Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.881 / SU B: 9.437 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.395 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEROCHEMICALLY.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.34 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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