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Yorodumi- PDB-3ed8: Application of the superfolder YFP bimolecular fluorescence compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ed8 | ||||||
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Title | Application of the superfolder YFP bimolecular fluorescence complementation for studying protein-protein interactions in vitro | ||||||
Components | yellow fluorescence protein | ||||||
Keywords | LUMINESCENT PROTEIN / superfolder / bimolecular fluorescence complementation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Ottmann, C. / Weyand, M. | ||||||
Citation | Journal: Biol.Chem. / Year: 2009 Title: Applicability of superfolder YFP bimolecular fluorescence complementation in vitro. Authors: Ottmann, C. / Weyand, M. / Wolf, A. / Kuhlmann, J. / Ottmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ed8.cif.gz | 226.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ed8.ent.gz | 185.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ed8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/3ed8 ftp://data.pdbj.org/pub/pdb/validation_reports/ed/3ed8 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 29339.270 Da / Num. of mol.: 5 Mutation: S30R,Y39I,F64L,F99S,N105K,E111V,I128T,Y145F,M153T,V163A,K166T,I167V,I171V,S205T,A206V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli) / References: UniProt: P42212*PLUS #2: Water | ChemComp-HOH / | Sequence details | GLY65,TYR66,GLY67 CIRCULARIZ | |
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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: 3.2 Å3/Da / Density % sol: 61.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris/HCl pH 8.5, 20 % ethanol, 12 % TCEP , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9781 Å |
Detector | Type: MAR CCD 225 mm / Detector: CCD / Date: Aug 25, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9781 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→45.98 Å / Num. all: 52991 / Num. obs: 52991 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 61.544 Å2 / Rsym value: 0.111 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 14.8 % / Mean I/σ(I) obs: 4.16 / Num. unique all: 5389 / Rsym value: 0.64 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→45.98 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 21.084 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.254 / 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: 35.262 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→45.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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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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