[English] 日本語
Yorodumi- PDB-2o2b: Spectroscopic and Structural Study of the Heterotropic Linkage be... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o2b | ||||||
---|---|---|---|---|---|---|---|
Title | Spectroscopic and Structural Study of the Heterotropic Linkage between Halide and Proton Ion Binding to Gfp Proteins: E2(GFP)-I Complex | ||||||
Components | Green fluorescent protein | ||||||
Keywords | LUMINESCENT PROTEIN / LUMINESCENCE / GREEN FLUORESCENT PROTEIN / GFP / E2 / BIOLUMINESCENCE / PHOTOACTIVE PROTEIN / FLUORESCENT CHLORIDE / BROMIDE / IODINE / HALOGEN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Garau, G. | ||||||
Citation | Journal: Biophys.J. / Year: 2007 Title: Spectroscopic and Structural Study of Proton and Halide Ion Cooperative Binding to GFP. Authors: Arosio, D. / Garau, G. / Ricci, F. / Marchetti, L. / Bizzarri, R. / Beltram, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2o2b.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2o2b.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 2o2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o2b_validation.pdf.gz | 434.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2o2b_full_validation.pdf.gz | 437.3 KB | Display | |
Data in XML | 2o2b_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 2o2b_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/2o2b ftp://data.pdbj.org/pub/pdb/validation_reports/o2/2o2b | HTTPS FTP |
-Related structure data
Related structure data | 2h6vSC 2o24C 2o29C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27518.010 Da / Num. of mol.: 1 / Mutation: F64L, T203Y, H231L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 | ||
---|---|---|---|
#2: Chemical | ChemComp-IOD / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.51 % |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 5 Details: 14% (W/V) PEG 3350, 100 MM NH4 ACETATE, 0.2 M NH4I, PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 100K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54178 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→46.499 Å / Num. obs: 16918 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.94→2.04 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.438 / % possible all: 91.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2H6V Resolution: 1.94→18.66 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.963 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.641 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→18.66 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.94→1.99 Å / Total num. of bins used: 20
|