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Yorodumi- PDB-3t0x: Fluorogen Activating Protein M8VLA4(S55P) in complex with dimethy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t0x | |||||||||
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Title | Fluorogen Activating Protein M8VLA4(S55P) in complex with dimethylindole red | |||||||||
Components | Immunoglobulin variable lambda domain M8VLA4(S55P) | |||||||||
Keywords | DYE-BINDING PROTEIN / immunoglobulin fold / fluorogen activation / dimethylindole red | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-DIW Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | |||||||||
Authors | Stanfield, R. / Senutovitch, N. / Bhattacharyya, S. / Rule, G. / Wilson, I.A. / Armitage, B. / Waggoner, A.S. / Berget, P. | |||||||||
Citation | Journal: Biochemistry / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t0x.cif.gz | 98 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t0x.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 3t0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t0/3t0x ftp://data.pdbj.org/pub/pdb/validation_reports/t0/3t0x | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 13214.251 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pAK400 / Production host: Escherichia coli (E. coli) / Strain (production host): MachTI #2: Chemical | ChemComp-DIW / | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.25M ammonium sulfate, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.722 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 18, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.722 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→37.34 Å / Num. all: 20018 / Num. obs: 20018 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 26.6 Å2 / Rsym value: 8.7 / Net I/σ(I): 35.5 |
Reflection shell | Resolution: 1.96→1.98 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 977 / Rsym value: 54.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→37.3 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 23.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.727 Å2 / ksol: 0.373 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.96→37.3 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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