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Yorodumi- PDB-8a5s: Crystal structure of light-activated DNA-binding protein EL222 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a5s | ||||||||||||
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Title | Crystal structure of light-activated DNA-binding protein EL222 from Erythrobacter litoralis crystallized in dark, measured illuminated. | ||||||||||||
Components | Light-activated DNA-binding protein EL222 | ||||||||||||
Keywords | TRANSCRIPTION / Light-activated transcription factor / DNA binding protein / LOV domain | ||||||||||||
Function / homology | Function and homology information nucleotide binding / regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||||||||
Biological species | Erythrobacter litoralis HTCC2594 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||||||||
Authors | Koval, T. / Chaudhari, A. / Fuertes, G. / Andersson, I. / Dohnalek, J. | ||||||||||||
Funding support | Czech Republic, European Union, 3items
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Citation | Journal: To Be Published Title: EL222 from Erythrobacter litoralis. Authors: Chaudhari, A. / Koval, T. / Andersson, I. / Dohnalek, J. / Fuertes, G. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a5s.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a5s.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8a5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a5s_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8a5s_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8a5s_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 8a5s_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/8a5s ftp://data.pdbj.org/pub/pdb/validation_reports/a5/8a5s | HTTPS FTP |
-Related structure data
Related structure data | 8a5rC 3p7nS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 23210.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Oxidation of His101 to 2-oxo-histidine Source: (gene. exp.) Erythrobacter litoralis HTCC2594 (bacteria) Strain: HTCC2594 / Gene: ELI_04755 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2NB98 |
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-Non-polymers , 5 types, 230 molecules
#2: Chemical | ChemComp-FMN / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MES / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 1.96 Å3/Da / Density % sol: 37.33 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 21% (w/v) PEG 8000, 0.22 M MgCl2, 0.11 M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: Excillum MetalJet D2 70 kV / Wavelength: 1.3418 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Jun 10, 2020 / Details: HELIOS optics for MetalJet |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→43.57 Å / Num. obs: 16065 / % possible obs: 99.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 9.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.055 / Rrim(I) all: 0.129 / Χ2: 1.01 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 955 / CC1/2: 0.636 / Rpim(I) all: 0.418 / Rrim(I) all: 0.881 / Χ2: 0.93 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P7N Resolution: 1.85→40.223 Å / Cor.coef. Fo:Fc: 0.961 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.149 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.705 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→40.223 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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