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Yorodumi- PDB-5vik: Crystal structure of monomeric near-infrared fluorescent protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vik | ||||||
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Title | Crystal structure of monomeric near-infrared fluorescent protein miRFP703 | ||||||
Components | near-infrared fluorescent protein miRFP703 | ||||||
Keywords | FLUORESCENT PROTEIN / near-infrared fluorescent protein / biliverdin / phytochrome / RpBphP1 | ||||||
Function / homology | Function and homology information detection of visible light / photoreceptor activity / regulation of DNA-templated transcription / ATP binding Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Pletnev, S. | ||||||
Citation | Journal: Chem Sci / Year: 2017 Title: Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies. Authors: Baloban, M. / Shcherbakova, D.M. / Pletnev, S. / Pletnev, V.Z. / Lagarias, J.C. / Verkhusha, V.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vik.cif.gz | 150.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vik.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/5vik ftp://data.pdbj.org/pub/pdb/validation_reports/vi/5vik | HTTPS FTP |
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-Related structure data
Related structure data | 5viqC 5vivC 4xtqS C: citing same article (ref.) 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
#1: Protein | Mass: 34556.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Production host: Escherichia coli (E. coli) / References: UniProt: B3Q7C0*PLUS |
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#2: Chemical | ChemComp-BLA / |
#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: 1.79 Å3/Da / Density % sol: 31.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.08M Na Citrate pH 5.0, 24% v/v Jeffamine ED-2001 pH 7.0 0.4% n-octyl-beta-D-glucopyranoside |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→29.93 Å / Num. obs: 53575 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.033 / Rrim(I) all: 0.063 / Χ2: 0.898 / Net I/σ(I): 13.6 / Num. measured all: 197471 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XTQ Resolution: 1.35→29.93 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.979 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.055 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.64 Å2 / Biso mean: 20.485 Å2 / Biso min: 8.87 Å2
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Refinement step | Cycle: final / Resolution: 1.35→29.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.351→1.386 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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