+Open data
-Basic information
Entry | Database: PDB / ID: 4o8g | ||||||
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Title | Structure of Infrared Fluorescent Protein 1.4 | ||||||
Components | Bacteriophytochrome | ||||||
Keywords | FLUORESCENT PROTEIN / Figure-of-Eight Knot / PAS / GAF / near-IR Fluorescence / Biliverdin | ||||||
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 / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans R1 (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.652 Å | ||||||
Authors | Bhattacharya, S. / Forest, K.T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Origins of fluorescence in evolved bacteriophytochromes. Authors: Bhattacharya, S. / Auldridge, M.E. / Lehtivuori, H. / Ihalainen, J.A. / Forest, K.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o8g.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o8g.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 4o8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/4o8g ftp://data.pdbj.org/pub/pdb/validation_reports/o8/4o8g | HTTPS FTP |
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-Related structure data
Related structure data | 4ijgC 3s7nS S: Starting model for refinement C: citing same article (ref.) |
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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: 35888.961 Da / Num. of mol.: 1 Mutation: D207H, A288V, V186M, I208T, M54V, L311K, T135I, L195M, H196Q, G119A, Y307E, L314G, V318R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 Gene: bphP, DR_A0050 / Plasmid: pet21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RZA4 |
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#2: Chemical | ChemComp-LBV / |
#3: Chemical | ChemComp-LBW / |
#4: 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: 2.38 Å3/Da / Density % sol: 48.35 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Mother liquor 6% PEG 4000, 10% glycerol, 0.07 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.6 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 21, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.6 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→30 Å / Num. all: 40554 / Num. obs: 38000 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.068 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.65→1.7 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 8.84 / Rsym value: 0.219 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3S7N Resolution: 1.652→24.04 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.662 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.1 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.579 Å2
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Refine analyze | Luzzati coordinate error free: 0.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.652→24.04 Å
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Refine LS restraints |
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