+Open data
-Basic information
Entry | Database: PDB / ID: 7lug | ||||||
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Title | Crystal structure of the pnRFP B30Y mutant | ||||||
Components | Red Fluorescent pnRFP B30Y mutant | ||||||
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: 1.95 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 | 7lug.cif.gz | 62 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lug.ent.gz | 42.9 KB | Display | PDB format |
PDBx/mmJSON format | 7lug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/7lug ftp://data.pdbj.org/pub/pdb/validation_reports/lu/7lug | HTTPS FTP |
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-Related structure data
Related structure data | 7lqoSC 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: 29741.689 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: 2.02 Å3/Da / Density % sol: 38.97 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop / Details: Sodium phosphate, citric acid, PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 20, 2018 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→41.85 Å / Num. obs: 17539 / % possible obs: 99.3 % / Redundancy: 3.56 % / CC1/2: 0.998 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.95→2 Å / Num. unique obs: 1245 / CC1/2: 0.814 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7LQO Resolution: 1.95→41.85 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.451 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.142 / 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: 66.16 Å2 / Biso mean: 32.588 Å2 / Biso min: 22.66 Å2
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Refinement step | Cycle: final / Resolution: 1.95→41.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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