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Yorodumi- PDB-6grm: Structure of GFPmut2 crystallized at pH 6 and transferred to pH 9 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6grm | ||||||
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Title | Structure of GFPmut2 crystallized at pH 6 and transferred to pH 9 | ||||||
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: 2.3 Å | ||||||
Authors | Lolli, G. / Raboni, S. / Pasqualetto, E. / Campanini, B. / Mozzarelli, A. / Bettati, S. / 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 | 6grm.cif.gz | 61.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6grm.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 6grm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/6grm ftp://data.pdbj.org/pub/pdb/validation_reports/gr/6grm | HTTPS FTP |
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-Related structure data
Related structure data | 6go8C 6go9C 6gqgC 6gqhC 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: 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: 1.84 Å3/Da / Density % sol: 33.33 % Description: Crystal suffered from soaking in MPD 85% and change in pH from 6 to 9 |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6 / Details: MPD 45% |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2009 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.3→40.13 Å / Num. obs: 9288 / % possible obs: 97.9 % / Redundancy: 3.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.053 / Rrim(I) all: 0.104 / Net I/σ(I): 7.9 | ||||||||||||||||||||||||
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: 2.3→40.126 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.72 Å2 / Biso mean: 34.4378 Å2 / Biso min: 11.55 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→40.126 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: 3
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