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Yorodumi- PDB-5ajg: Structure of Infrared Fluorescent Protein IFP1.4 AT 1.11 Angstrom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ajg | ||||||
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Title | Structure of Infrared Fluorescent Protein IFP1.4 AT 1.11 Angstrom resolution | ||||||
Components | BACTERIOPHYTOCHROME | ||||||
Keywords | FLUORESCENT PROTEIN | ||||||
Function / homology | Function and homology information osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | DEINOCOCCUS RADIODURANS (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å | ||||||
Authors | Lafaye, C. / Shu, X. / Royant, A. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Structural Determinants of Improved Fluorescence in a Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins: Insights from Continuum Electrostatic Calculations and Molecular Dynamics Simulations. Authors: Feliks, M. / Lafaye, C. / Shu, X. / Royant, A. / Field, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ajg.cif.gz | 149.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ajg.ent.gz | 118.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ajg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ajg_validation.pdf.gz | 777.7 KB | Display | wwPDB validaton report |
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Full document | 5ajg_full_validation.pdf.gz | 781 KB | Display | |
Data in XML | 5ajg_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 5ajg_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/5ajg ftp://data.pdbj.org/pub/pdb/validation_reports/aj/5ajg | HTTPS FTP |
-Related structure data
Related structure data | 4cqhS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 35957.035 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-321 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant) Plasmid: PBAD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RZA4, histidine kinase |
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#2: Chemical | ChemComp-LBV / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.65 % / Description: NONE |
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Crystal grow | pH: 5 / Details: 26% PEG 400, 0.1 M SODIUM ACETATE PH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.11→38.4 Å / Num. obs: 121711 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 14.239 Å2 / Rsym value: 0.03 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.11→1.13 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2 / Rsym value: 0.62 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CQH Resolution: 1.11→38.43 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.803 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COVALENT BOND BETWEEN ATOM SG OF CYS A24 AND ATOM CBA1 OF CHROMOPHORE LBV B1
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.135 Å2
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Refinement step | Cycle: LAST / Resolution: 1.11→38.43 Å
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Refine LS restraints |
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