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Yorodumi- PDB-2v1b: N- and C-terminal helices of oat LOV2 (404-546) are involved in l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v1b | ||||||
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Title | N- and C-terminal helices of oat LOV2 (404-546) are involved in light-induced signal transduction (room temperature (293K) light structure of LOV2 (404-546)) | ||||||
Components | NPH1-1 | ||||||
Keywords | TRANSFERASE / LOV2 / KINASE / ATP-BINDING / AVENA SATIVA / SERINE/THREONINE-PROTEIN KINASE / LIGHT-INDUCED SIGNAL TRANSDUCTION / PHOTOTROPIN1 / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information blue light photoreceptor activity / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | AVENA SATIVA (oats) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Halavaty, A.S. / Moffat, K. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: N- and C-Terminal Flanking Regions Modulate Light-Induced Signal Transduction in the Lov2 Domain of the Blue Light Sensor Phototropin 1 from Avena Sativa. Authors: Halavaty, A.S. / Moffat, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v1b.cif.gz | 49.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v1b.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 2v1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v1b_validation.pdf.gz | 765.9 KB | Display | wwPDB validaton report |
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Full document | 2v1b_full_validation.pdf.gz | 769 KB | Display | |
Data in XML | 2v1b_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 2v1b_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/2v1b ftp://data.pdbj.org/pub/pdb/validation_reports/v1/2v1b | HTTPS FTP |
-Related structure data
Related structure data | 2v0uSC 2v0wC 2v1aC 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: 16666.840 Da / Num. of mol.: 1 / Fragment: LIGHT, OXYGEN, VOLTAGE DOMAIN, RESIDUES 404-546 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AVENA SATIVA (oats) / Plasmid: PHIS-GB1-PARALLEL1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O49003 |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Sequence details | PHE403 (VECTOR RESIDUE) DOES NOT BELONG TO LOV2 SEQUENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.01 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 |
Detector | Type: ADSC CCD / Detector: CCD / Details: BENT CONICAL SI-MIRROR (RH COATED) |
Radiation | Monochromator: BENT GE(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 19930 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.4 / % possible all: 96 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V0U Resolution: 1.55→16.12 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.029 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→16.12 Å
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Refine LS restraints |
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