+Open data
-Basic information
Entry | Database: PDB / ID: 4nxb | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of iLOV-I486(2LT) at pH 7.0 | ||||||
Components | Phototropin-2 | ||||||
Keywords | FLAVOPROTEIN / FLUORESCENT PROTEIN / FMN Binding | ||||||
Function / homology | Function and homology information chloroplast relocation / negative regulation of anion channel activity by blue light / phototropism / stomatal movement / response to blue light / blue light photoreceptor activity / plastid / circadian rhythm / FMN binding / kinase activity ...chloroplast relocation / negative regulation of anion channel activity by blue light / phototropism / stomatal movement / response to blue light / blue light photoreceptor activity / plastid / circadian rhythm / FMN binding / kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / Golgi apparatus / ATP binding / identical protein binding / membrane / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.561 Å | ||||||
Authors | Wang, J. / Li, J. / Liu, X. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2014 Title: Significant expansion of fluorescent protein sensing ability through the genetic incorporation of superior photo-induced electron-transfer quenchers. Authors: Liu, X. / Jiang, L. / Li, J. / Wang, L. / Yu, Y. / Zhou, Q. / Lv, X. / Gong, W. / Lu, Y. / Wang, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4nxb.cif.gz | 104.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4nxb.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 4nxb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nxb_validation.pdf.gz | 972.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4nxb_full_validation.pdf.gz | 977.4 KB | Display | |
Data in XML | 4nxb_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 4nxb_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/4nxb ftp://data.pdbj.org/pub/pdb/validation_reports/nx/4nxb | HTTPS FTP |
-Related structure data
Related structure data | 4nx2C 4nxeC 4nxfC 4nxgC 4eesS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13969.408 Da / Num. of mol.: 2 / Fragment: LOV DOMAIN, UNP Residues 388-496 / Mutation: S394T, S409G, I452T, F470L, M475V, I486Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHOT2, CAV1, KIN7, NPL1, At5g58140, K21L19.6 / Production host: Escherichia coli (E. coli) References: UniProt: P93025, non-specific serine/threonine protein kinase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | RESIDUES C426A IS MUTAGENESI | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.37 % |
---|---|
Crystal grow | Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 200 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU Saturn 944HG / Detector: CCD / Date: Jan 3, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. all: 7944 / Num. obs: 7658 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.55→2.59 Å / Redundancy: 1.9 % / Num. unique all: 383 / % possible all: 94.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EES Resolution: 2.561→31.455 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8043 / SU ML: 0.31 / σ(F): 1.99 / Phase error: 27.18 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 45.31 Å2 / Biso mean: 22.7171 Å2 / Biso min: 9.49 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.561→31.455 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -2.7877 Å / Origin y: -4.4979 Å / Origin z: -10.0653 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: ALL |