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Yorodumi- PDB-2dug: crystal structure of a green fluorescent protein S65T/H148N at pH 5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dug | ||||||
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Title | crystal structure of a green fluorescent protein S65T/H148N at pH 5 | ||||||
Components | Green fluorescent protein | ||||||
Keywords | LUMINESCENT PROTEIN / excited state proton transfer / very short hydrogen bond / green fluorescent protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Shu, X. / Remington, S.J. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Ultrafast excited-state dynamics in the green fluorescent protein variant S65T/H148D. 1. Mutagenesis and structural studies. Authors: Shu, X. / Kallio, K. / Shi, X. / Abbyad, P. / Kanchanawong, P. / Childs, W. / Boxer, S.G. / Remington, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dug.cif.gz | 58.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dug.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 2dug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/2dug ftp://data.pdbj.org/pub/pdb/validation_reports/du/2dug | HTTPS FTP |
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-Related 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: 26906.346 Da / Num. of mol.: 1 / Mutation: S65T, H148N, Q80R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 |
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#2: Water | ChemComp-HOH / |
Sequence details | RESIDUE SER 65 IS MUTATED TO THR 65. THR 65, TYR 66 AND GLY 67 ARE MODIFIED TO MAKE CHROMOPHOR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 50mM Li2SO4, 100mM Acetate pH 9.5, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. all: 43567 / Num. obs: 43438 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.4→1.45 Å / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→6 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.4→6 Å
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