+Open data
-Basic information
Entry | Database: PDB / ID: 4nxf | ||||||
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Title | Crystal structure of iLOV-I486(2LT) at pH 8.0 | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.766 Å | ||||||
Authors | Wang, J. / Liu, X. / Li, J. | ||||||
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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nxf.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nxf.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 4nxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nxf_validation.pdf.gz | 986.1 KB | Display | wwPDB validaton report |
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Full document | 4nxf_full_validation.pdf.gz | 986.8 KB | Display | |
Data in XML | 4nxf_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 4nxf_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/4nxf ftp://data.pdbj.org/pub/pdb/validation_reports/nx/4nxf | HTTPS FTP |
-Related structure data
Related structure data | 4nx2C 4nxbC 4nxeC 4nxgC 4eesS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.96 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: protein sample (20-30 mg/ml) in 20mM Tris, pH 8.0, 50mM NaCl, equal volume of reservoir solution (0.2M Ammonium acetate, 0.1M Tris pH 8.0, 16% w/v Polyethylene glycol 10000), VAPOR ...Details: protein sample (20-30 mg/ml) in 20mM Tris, pH 8.0, 50mM NaCl, equal volume of reservoir solution (0.2M Ammonium acetate, 0.1M Tris pH 8.0, 16% w/v Polyethylene glycol 10000), VAPOR DIFFUSION, SITTING DROP, temperature 289.0 K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.766→50 Å / Num. all: 22542 / Num. obs: 21167 / % possible obs: 93.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.766→1.8 Å / Redundancy: 3.6 % / Num. unique all: 1066 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EES Resolution: 1.766→24.203 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8606 / SU ML: 0.16 / σ(F): 1.43 / Phase error: 21.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.74 Å2 / Biso mean: 24.1841 Å2 / Biso min: 11.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.766→24.203 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Origin x: -3.5914 Å / Origin y: -2.4953 Å / Origin z: 60.3517 Å
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Refinement TLS group | Selection details: ALL |