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Yorodumi- PDB-7lqo: Crystal structure of a genetically encoded red fluorescent peroxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lqo | ||||||
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Title | Crystal structure of a genetically encoded red fluorescent peroxynitrite biosensor, pnRFP | ||||||
Components | red fluorescent peroxynitrite biosensor pnRFP | ||||||
Keywords | FLUORESCENT PROTEIN / Red fluorescent protein / Peroxynitrite / Biosensor / Boronophenylalanine. | ||||||
Function / homology | PHOSPHATE ION Function and homology information | ||||||
Biological species | Discosoma sp. (sea anemone) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Huang, M. / Ng, H.L. / Pang, Y. / Zhang, S. / Fan, Y. / Yeh, H. / Xiong, Y. / Li, X. / Ai, H. | ||||||
Citation | Journal: To Be Published Title: Development, Characterization, and Structural Analysis of a Genetically Encoded Red Fluorescent Peroxynitrite Biosensor Authors: Pang, Y. / Huang, M. / Zhang, S. / Fan, Y. / Yeh, H. / Xiong, Y. / Li, X. / Ng, H.L. / Ai, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lqo.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lqo.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 7lqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/7lqo ftp://data.pdbj.org/pub/pdb/validation_reports/lq/7lqo | HTTPS FTP |
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-Related structure data
Related structure data | 7lugC 5f9gS 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
#1: Protein | Mass: 29769.506 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia phage EcSzw-2 (virus) |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.68 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / Details: Sodium Phosphate, citric acid, PEG 400. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.115834 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115834 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→41.81 Å / Num. obs: 13553 / % possible obs: 95.1 % / Redundancy: 3.74 % / CC1/2: 0.998 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.1→2.16 Å / Num. unique obs: 831 / CC1/2: 0.805 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5f9g Resolution: 2.1→41.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.852 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.12 Å2 / Biso mean: 36.343 Å2 / Biso min: 17.54 Å2
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Refinement step | Cycle: final / Resolution: 2.1→41.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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