+Open data
-Basic information
Entry | Database: PDB / ID: 7amu | ||||||
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Title | Crystal structure of rsEGFP2 T204A in its fluorescent on-state | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / Enhanced GFP / Reversibly Photoswitchable Fluorescent Protein / Photoconvertible FP | ||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Moreno-Chicano, T. / Schlichting, I. / Hartmann, E. / Zala, N. / Colletier, J.-P. / Weik, M. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of rsEGFP2 in its fluorescent on-state at pH 8.0 Authors: Moreno-Chicano, T. / Schlichting, I. / Hartmann, E. / Zala, N. / Colletier, J.-P. / Weik, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7amu.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7amu.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 7amu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/7amu ftp://data.pdbj.org/pub/pdb/validation_reports/am/7amu | HTTPS FTP |
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-Related structure data
Related structure data | 5o89S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28502.176 Da / Num. of mol.: 1 / Mutation: F64L, S65A, Q69L, V163S, A206K, H231L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P42212 | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 11 / Details: Ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→46.58 Å / Num. obs: 28151 / % possible obs: 99.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 29.06 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.047 / Χ2: 0.96 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.64→1.67 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1356 / CC1/2: 0.596 / Rrim(I) all: 1.547 / Χ2: 0.85 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5o89 Resolution: 1.64→41.57 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.015 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 109.32 Å2 / Biso mean: 33.375 Å2 / Biso min: 18.66 Å2
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Refinement step | Cycle: final / Resolution: 1.64→41.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.681 Å / Rfactor Rfree error: 0
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