+Open data
-Basic information
Entry | Database: PDB / ID: 1bfp | ||||||
---|---|---|---|---|---|---|---|
Title | BLUE VARIANT OF GREEN FLUORESCENT PROTEIN | ||||||
Components | BLUE FLUORESCENT PROTEIN | ||||||
Keywords | LUMINESCENCE / FLUORESCENT PROTEIN / BLUE EMISSION / MUTANT / FLUOROPHORE / BIOLUMINESCENSE | ||||||
Function / homology | Function and homology information serine-type endopeptidase inhibitor activity / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Wachter, R.M. / Remington, S.J. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Crystal structure and photodynamic behavior of the blue emission variant Y66H/Y145F of green fluorescent protein. Authors: Wachter, R.M. / King, B.A. / Heim, R. / Kallio, K. / Tsien, R.Y. / Boxer, S.G. / Remington, S.J. #1: Journal: Curr.Biol. / Year: 1996 Title: Engineering Green Fluorescent Protein for Improved Brightness, Longer Wavelengths and Fluorescence Resonance Energy Transfer Authors: Heim, R. / Tsien, R.Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bfp.cif.gz | 55.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bfp.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bfp_validation.pdf.gz | 371.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1bfp_full_validation.pdf.gz | 382.6 KB | Display | |
Data in XML | 1bfp_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 1bfp_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/1bfp ftp://data.pdbj.org/pub/pdb/validation_reports/bf/1bfp | HTTPS FTP |
-Related structure data
Related structure data | 1emaS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26891.338 Da / Num. of mol.: 1 / Mutation: S65, H66, AND G67 ARE REPLACED WITH IIC 66, Y145F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Description: THE N-TERMINAL HIS-TAG HAS BEEN REMOVED / Plasmid: PRSETB (INVITROGEN) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3) / References: UniProt: P42212 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.7 % / Description: ISOMORPHOUS REPLACEMENT | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / pH: 4.5 Details: PROTEIN WAS CRYSTALLIZED AT 4 DEGC FROM 100MM SODIUM ACETATE PH 4.5 AND 10-12% PEG3400., temperature 277K | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Sep 19, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 12044 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 2.64 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.1→2.26 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 2.24 / % possible all: 64 |
Reflection | *PLUS Num. measured all: 31786 |
Reflection shell | *PLUS % possible obs: 65 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EMA Resolution: 2.1→20 Å / Isotropic thermal model: TNT / σ(F): 0 / Stereochemistry target values: TNT
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 300 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Version: 5F / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.181 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|