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Yorodumi- PDB-8afk: Structure of iRFP variant C15S/N136R/V256C in complex with phycoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8afk | ||||||
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Title | Structure of iRFP variant C15S/N136R/V256C in complex with phycocyanobilin | ||||||
Components | Near-infrared fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / iRFP / phytochrome / phycocyanobilin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris CGA009 (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.015 Å | ||||||
Authors | Remeeva, A. / Kovalev, K. / Gushchin, I. / Fonin, A. / Turoverov, K. / Stepanenko, O. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of iRFP variant C15S/N136R/V256C in complex with phycocyanobilin Authors: Remeeva, A. / Kovalev, K. / Gushchin, I. / Fonin, A. / Turoverov, K. / Stepanenko, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8afk.cif.gz | 125 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8afk.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 8afk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/8afk ftp://data.pdbj.org/pub/pdb/validation_reports/af/8afk | HTTPS FTP |
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-Related structure data
Related structure data | 4e04S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34671.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris CGA009 (phototrophic) Gene: iRFP / Production host: Escherichia coli (E. coli) / References: UniProt: G1FNL7 #2: Chemical | #3: Water | ChemComp-HOH / | 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: 2.17 Å3/Da / Density % sol: 43.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% PEG1000 10% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.015→69.7 Å / Num. obs: 30361 / % possible obs: 75.4 % / Redundancy: 13.6 % / CC1/2: 0.9994 / Rpim(I) all: 0.03 / Net I/σ(I): 14.257 |
Reflection shell | Resolution: 2.015→2.182 Å / Num. unique obs: 1898 / CC1/2: 0.2832 / Rpim(I) all: 1.406 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 40000 / Resolution: 2.015→19.99 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.319 / SU Rfree Blow DPI: 0.235 / SU Rfree Cruickshank DPI: 0.239
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Displacement parameters | Biso max: 101.18 Å2 / Biso mean: 57.27 Å2 / Biso min: 30.84 Å2
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Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.015→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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