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- PDB-3t0w: Fluorogen activating protein M8VL in complex with dimethylindole red -
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Open data
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Basic information
Entry | Database: PDB / ID: 3t0w | |||||||||
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Title | Fluorogen activating protein M8VL in complex with dimethylindole red | |||||||||
![]() | immunoglobulin variable lambda domain | |||||||||
![]() | DYE-BINDING PROTEIN / immunoglobulin fold / fluorogen activation / dimethylindole red | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-DIW / Chem-PE3![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Stanfield, R. / Senutovitch, N. / Bhattacharyya, S. / Rule, G. / Wilson, I.A. / Armitage, B. / Waggoner, A.S. / Berget, P. | |||||||||
![]() | ![]() Title: A variable light domain fluorogen activating protein homodimerizes to activate dimethylindole red. Authors: Senutovitch, N. / Stanfield, R.L. / Bhattacharyya, S. / Rule, G.S. / Wilson, I.A. / Armitage, B.A. / Waggoner, A.S. / Berget, P.B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.3 KB | Display | ![]() |
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PDB format | ![]() | 85.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 13204.214 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-PE3 / | #4: Chemical | ChemComp-DIW / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 35% PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→41.8 Å / Num. all: 35526 / Num. obs: 35526 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 11.7 Å2 / Rsym value: 8.7 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 1758 / Rsym value: 53.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.168 Å2 / ksol: 0.338 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.501→41.766 Å
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Refine LS restraints |
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LS refinement shell |
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