+Open data
-Basic information
Entry | Database: PDB / ID: 6gqg | ||||||
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Title | Structure of GFPmut2 crystallized at pH 8.5 | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / beta barrel / bioluminescence | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.792 Å | ||||||
Authors | Pasqualetto, E. / Lolli, G. / Battistutta, R. | ||||||
Citation | Journal: J.Phys.Chem.B / Year: 2018 Title: Insight into GFPmut2 pH Dependence by Single Crystal Microspectrophotometry and X-ray Crystallography. Authors: Lolli, G. / Raboni, S. / Pasqualetto, E. / Benoni, R. / Campanini, B. / Ronda, L. / Mozzarelli, A. / Bettati, S. / Battistutta, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gqg.cif.gz | 69.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gqg.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 6gqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/6gqg ftp://data.pdbj.org/pub/pdb/validation_reports/gq/6gqg | HTTPS FTP |
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-Related structure data
Related structure data | 6go8C 6go9C 6gqhC 6grmC 1q4aS 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: 27433.920 Da / Num. of mol.: 1 Mutation: S65A, V68L, S72A; First six residues GSHIGP derive from the expression tag Source method: isolated from a genetically manipulated source Details: S65A, V68L, S72A; First six residues GSHIGP derive from the expression tag Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / 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: 2.03 Å3/Da / Density % sol: 39.31 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 8.5 / Details: 0.2 M CaCl2, 19% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.792→46.5 Å / Num. obs: 21218 / % possible obs: 98.3 % / Redundancy: 6.3 % / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Rsym value: 0.07 / Net I/av σ(I): 9.1 / Net I/σ(I): 18 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q4A Resolution: 1.792→46.5 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.01
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.96 Å2 / Biso mean: 24.0383 Å2 / Biso min: 9.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.792→46.5 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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