[English] 日本語
Yorodumi- PDB-5j2o: Crystal structure of the cyan fluorescence protein Cerulean S175G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j2o | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the cyan fluorescence protein Cerulean S175G mutant | |||||||||
Components | Green fluorescent protein | |||||||||
Keywords | FLUORESCENT PROTEIN / Cerulean / Cyan Fluorescent Protein | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Aequorea victoria (jellyfish) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Park, S.-W. / Kang, S. / Yoon, T.-S. | |||||||||
Funding support | Korea, Republic Of, 1items
| |||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2016 Title: Crystal structure of the cyan fluorescent protein Cerulean-S175G Authors: Park, S.-W. / Kang, S. / Yoon, T.-S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5j2o.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5j2o.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 5j2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/5j2o ftp://data.pdbj.org/pub/pdb/validation_reports/j2/5j2o | HTTPS FTP |
---|
-Related structure data
Related structure data | 2ydzS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27588.092 Da / Num. of mol.: 1 / Mutation: F65L/Y145A/N146I/H148D/M153T/V163A/S175G/H231L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODONPLUS(DE3) / References: UniProt: P42212 |
---|---|
#2: Water | ChemComp-HOH / |
Sequence details | 1. S72A IS MUTAGENESIS ACCORDING TO DATABASE P42212 (GFP_AEQVI) 2. CHROMOPHORE RESULTING FROM ...1. S72A IS MUTAGENESI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.81 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 16% PEG 8000, 0.1M MGCL2, 0.1M HEPES PH 7.5 / PH range: 7.0-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2015 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→35.053 Å / Num. obs: 36842 / % possible obs: 99.77 % / Redundancy: 7 % / Rsym value: 0.081 / Net I/av σ(I): 2.2 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 0.249 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 9 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ydz Resolution: 1.5→35.053 Å / Cross valid method: FREE R-VALUE / ESU R Free: 0.1878 / Phase error: 96.33 / Details: add hydrogene
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 0.1411 Å2 / ksol: 0.9725 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.01 Å2 / Biso mean: 12.8524 Å2 / Biso min: 3.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→35.053 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
|