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Yorodumi- PDB-2q6p: The Chemical Control of Protein Folding: Engineering a Superfolde... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q6p | ||||||
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Title | The Chemical Control of Protein Folding: Engineering a Superfolder Green Fluorescent Protein | ||||||
Components | Green fluorescent protein mutant 3 | ||||||
Keywords | LUMINESCENT PROTEIN / GFP / Noncanonical amino acid / superfolder | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Steiner, T. / Hess, P. / Bae, J.H. / Wiltschi, B. / Moroder, L. / Budisa, N. | ||||||
Citation | Journal: Plos One / Year: 2008 Title: Synthetic biology of proteins: tuning GFPs folding and stability with fluoroproline. Authors: Steiner, T. / Hess, P. / Bae, J.H. / Wiltschi, B. / Moroder, L. / Budisa, N. | ||||||
History |
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Remark 999 | SEQUENCE The residues THR 65, TYR 66 and GLY 67 constitute the chromophore CRO 66. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q6p.cif.gz | 62 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q6p.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 2q6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/2q6p ftp://data.pdbj.org/pub/pdb/validation_reports/q6/2q6p | HTTPS FTP |
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-Related structure data
Related structure data | 1emgS 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: 27091.275 Da / Num. of mol.: 1 / Mutation: F64L,A72S,Q80R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: Q93125, UniProt: P42212*PLUS |
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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: 2.15 Å3/Da / Density % sol: 42.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 20, 2004 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46 Å / Num. all: 13465 / Num. obs: 12901 / % possible obs: 95.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 6.8 Å2 |
Reflection shell | Resolution: 2.1→2.17 Å / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EMG Resolution: 2.1→19.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 445648.094 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 82.543 Å2 / ksol: 0.56 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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