[English] 日本語
Yorodumi- PDB-7zqu: A fast recovering full-length LOV protein (DsLOV) from the marine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zqu | ||||||
---|---|---|---|---|---|---|---|
Title | A fast recovering full-length LOV protein (DsLOV) from the marine phototrophic bacterium Dinoroseobacter shibae (Dark state) - C72A mutant | ||||||
Components | Putative blue-light photoreceptor | ||||||
Keywords | SIGNALING PROTEIN / LOV domain / short LOV / PAS domain / Dimerization / Signaling blue light photoreceptor | ||||||
Function / homology | PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAS repeat profile. / PAS domain / PAS domain superfamily / nucleotide binding / FLAVIN MONONUCLEOTIDE / Putative blue-light photoreceptor Function and homology information | ||||||
Biological species | Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Batra-Safferling, R. / Granzin, J. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: To Be Published Title: A fast recovering full-length LOV protein (DsLOV) from the marine phototrophic bacterium Dinoroseobacter shibae (Dark state) - C72A mutant Authors: Batra-Safferling, R. / Granzin, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7zqu.cif.gz | 76.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7zqu.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 7zqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zqu_validation.pdf.gz | 739.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7zqu_full_validation.pdf.gz | 739.4 KB | Display | |
Data in XML | 7zqu_validation.xml.gz | 7 KB | Display | |
Data in CIF | 7zqu_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/7zqu ftp://data.pdbj.org/pub/pdb/validation_reports/zq/7zqu | HTTPS FTP |
-Related structure data
Related structure data | 4kukS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16828.855 Da / Num. of mol.: 1 / Mutation: C72A Source method: isolated from a genetically manipulated source Details: C72A ENGINEERED MUTATION Source: (gene. exp.) Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria) Strain: DSM 16493 / NCIMB 14021 / DFL 12 / Gene: Dshi_2006 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A8LP63 |
---|---|
#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.6 Å3/Da |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, 0.2 M MgCl2, 20% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 6, 2014 |
Radiation | Monochromator: microfocus beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→41.84 Å / Num. obs: 11015 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 26.3 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.053 / Rrim(I) all: 0.136 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.75→1.78 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 593 / CC1/2: 0.462 / Rpim(I) all: 0.912 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KUK Resolution: 1.75→41.84 Å / SU ML: 0.2961 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.9122 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→41.84 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A
|