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Yorodumi- PDB-5viv: Crystal structure of monomeric near-infrared fluorescent protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5viv | ||||||
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Title | Crystal structure of monomeric near-infrared fluorescent protein miRFP670 | ||||||
Components | monomeric near-infrared fluorescent protein miRFP670 | ||||||
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 Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 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 | 5viv.cif.gz | 157.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5viv.ent.gz | 121.6 KB | Display | PDB format |
PDBx/mmJSON format | 5viv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/5viv ftp://data.pdbj.org/pub/pdb/validation_reports/vi/5viv | HTTPS FTP |
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-Related structure data
Related structure data | 5vikC 5viqC 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: 34534.871 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: A0A161I5N6*PLUS | ||||
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#2: Chemical | ChemComp-9UY / | ||||
#3: Chemical | ChemComp-9V1 / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | 9V1 is bound form of Billeverdin IXa, linked to the protein with two thioester bonds: one between ...9V1 is bound form of Billeverdin IXa, linked to the protein with two thioester bonds: one between the atom CBC of 9V1 and SG of CYS A20 and another between the atom CAC of 9V1 and SG of CYS A253. 9UY is also a bound form Billeverdin IXa. 9UY has only one thioester bond with the protein: between the atom CBC of 9UY and SG of CYS A253 | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3.4 M NaCl, 0.08 M Tris-HCl pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / 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: 1.33→30 Å / Num. obs: 69538 / % possible obs: 99.6 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.33→1.38 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.735 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XTQ Resolution: 1.33→29.6 Å / SU B: 2.034 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.053 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Displacement parameters | Biso mean: 26.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.33→29.6 Å
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LS refinement shell | Resolution: 1.33→1.37 Å
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