+Open data
-Basic information
Entry | Database: PDB / ID: 8y33 | ||||||
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Title | A near-infrared fluorescent protein of de novo backbone design | ||||||
Components | near-infrared fluorescent protein | ||||||
Keywords | DE NOVO PROTEIN / De novo backbone design / monomerization / near-infrared fluorescent protein | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Hu, X. / Xu, Y. | ||||||
Funding support | 1items
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Citation | Journal: Acs Synth Biol / Year: 2024 Title: Using Protein Design and Directed Evolution to Monomerize a Bright Near-Infrared Fluorescent Protein. Authors: Hu, X. / Xu, Y. / Yi, J. / Wang, C. / Zhu, Z. / Yue, T. / Zhang, H. / Wang, X. / Wu, F. / Xue, L. / Bai, L. / Liu, H. / Chen, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8y33.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8y33.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 8y33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/8y33 ftp://data.pdbj.org/pub/pdb/validation_reports/y3/8y33 | HTTPS FTP |
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-Related structure data
Related structure data | 8j1wC 8j1xC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21136.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-V8U / Mass: 586.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H38N4O6 / Feature type: SUBJECT OF INVESTIGATION |
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: 3.2 Å3/Da / Density % sol: 61.57 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 8.5 / Details: 3.5 M Sodium Formate, 0.1 M Tris, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97851 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97851 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 6001 / % possible obs: 95.65 % / Redundancy: 15 % / Biso Wilson estimate: 30.28 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.06 |
Reflection shell | Resolution: 2.9→3 Å / Num. unique obs: 499 / CC1/2: 0.792 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.9→34.69 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→34.69 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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