[English] 日本語
Yorodumi- PDB-1f09: CRYSTAL STRUCTURE OF THE GREEN FLUORESCENT PROTEIN (GFP) VARIANT ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f09 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE GREEN FLUORESCENT PROTEIN (GFP) VARIANT YFP-H148Q WITH TWO BOUND IODIDES | ||||||
Components | GREEN FLUORESCENT PROTEIN | ||||||
Keywords | LUMINESCENT PROTEIN / beta barrel / LUMINESCENCE / BIOLUMINESCENCE / PHOTOACTIVE PROTEIN / GREEN FLUORESCENT PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.14 Å | ||||||
Authors | Wachter, R.M. / Yarbrough, D. / Kallio, K. / Remington, S.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystallographic and energetic analysis of binding of selected anions to the yellow variants of green fluorescent protein. Authors: Wachter, R.M. / Yarbrough, D. / Kallio, K. / Remington, S.J. #1: Journal: CURR.BIOL. / Year: 1999 Title: Sensitivity of the Yellow Variant of Green Fluorescent Protein to Halides and Nitrate Authors: Wachter, R.M. / Remington, S.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1f09.cif.gz | 57.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1f09.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 1f09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/1f09 ftp://data.pdbj.org/pub/pdb/validation_reports/f0/1f09 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26951.408 Da / Num. of mol.: 1 / Mutation: S65G, V68L, S72A, Q80R, T203Y, H148Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: BL21DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.87 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 1550, sodium acetate, magnesium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.9 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 30, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30.1 Å / Num. all: 35882 / Num. obs: 10849 / % possible obs: 85.6 % / Redundancy: 3.31 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.519 / Num. unique all: 990 / % possible all: 79.6 |
Reflection | *PLUS Num. measured all: 35882 |
Reflection shell | *PLUS % possible obs: 79.6 % |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.14→30.1 Å / Stereochemistry target values: Engh & Huber
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→30.1 Å
| ||||||||||||||||
Refine LS restraints |
| ||||||||||||||||
Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Rfactor all: 0.204 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 2.83 |