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Yorodumi- PDB-4lqt: 1.10A resolution crystal structure of a superfolder green fluores... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lqt | ||||||
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Title | 1.10A resolution crystal structure of a superfolder green fluorescent protein (W57A) mutant | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / GFP / Chemical biology / allosteric activation / switchable enzyme / chemical rescue / mutation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å | ||||||
Authors | Lovell, S. / Xia, Y. / Vo, B. / Battaile, K.P. / Egan, C. / Karanicolas, J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation. Authors: Xia, Y. / DiPrimio, N. / Keppel, T.R. / Vo, B. / Fraser, K. / Battaile, K.P. / Egan, C. / Bystroff, C. / Lovell, S. / Weis, D.D. / Anderson, J.C. / Karanicolas, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lqt.cif.gz | 120.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lqt.ent.gz | 92.6 KB | Display | PDB format |
PDBx/mmJSON format | 4lqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/4lqt ftp://data.pdbj.org/pub/pdb/validation_reports/lq/4lqt | HTTPS FTP |
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-Related structure data
Related structure data | 4lquC 2b3pS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 27698.062 Da / Num. of mol.: 1 Mutation: S30R, Y39N, W57A, F99S, N105T, Y145F, M153T, V163A, I171V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P42212 | ||
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#2: Chemical | #3: 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: 2.15 Å3/Da / Density % sol: 42.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 40% (v/v) Isopropanol, 0.1 M Imidazole acid, 15% (w/v) PEG 8000, pH 6.5, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.8265 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8265 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→57.885 Å / Num. all: 93517 / Num. obs: 93517 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 11.25 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.1→1.12 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4593 / % possible all: 98.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B3P Resolution: 1.1→24.704 Å / Occupancy max: 1 / Occupancy min: 0.14 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.16 / Phase error: 13.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 46.34 Å2 / Biso mean: 15.3909 Å2 / Biso min: 7.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→24.704 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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