+Open data
-Basic information
Entry | Database: PDB / ID: 8q79 | ||||||
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Title | Structure of mBaoJin at pH 6.5 | ||||||
Components | mBaoJin | ||||||
Keywords | FLUORESCENT PROTEIN / mBaoJin | ||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Fluorescent protein Function and homology information | ||||||
Biological species | Cytaeis uchidae (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Samygina, V.R. / Subach, O.M. / Vlaskina, A.V. / Nikolaeva, A.Y. / Borshchevsky, V. / Qin, W. / Subach, F.V. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Nat.Methods / Year: 2024 Title: Bright and stable monomeric green fluorescent protein derived from StayGold. Authors: Zhang, H. / Lesnov, G.D. / Subach, O.M. / Zhang, W. / Kuzmicheva, T.P. / Vlaskina, A.V. / Samygina, V.R. / Chen, L. / Ye, X. / Nikolaeva, A.Y. / Gabdulkhakov, A. / Papadaki, S. / Qin, W. / ...Authors: Zhang, H. / Lesnov, G.D. / Subach, O.M. / Zhang, W. / Kuzmicheva, T.P. / Vlaskina, A.V. / Samygina, V.R. / Chen, L. / Ye, X. / Nikolaeva, A.Y. / Gabdulkhakov, A. / Papadaki, S. / Qin, W. / Borshchevskiy, V. / Perfilov, M.M. / Gavrikov, A.S. / Drobizhev, M. / Mishin, A.S. / Piatkevich, K.D. / Subach, F.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q79.cif.gz | 208.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q79.ent.gz | 159.7 KB | Display | PDB format |
PDBx/mmJSON format | 8q79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q79_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8q79_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8q79_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 8q79_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/8q79 ftp://data.pdbj.org/pub/pdb/validation_reports/q7/8q79 | HTTPS FTP |
-Related structure data
Related structure data | 8qbjC 8qddC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26841.123 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Fluorophore (CR2) is formed from G57Y58G59 residues of the peptide Source: (gene. exp.) Cytaeis uchidae (invertebrata) / Gene: CU17S / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8S0GSD4 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.48 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG8000, 0.1M NH4Acetate, 0.1M Na Cocadilate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97861 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 19, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97861 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→30 Å / Num. obs: 94189 / % possible obs: 97.7 % / Redundancy: 6.3 % / CC1/2: 0.99 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.45→1.49 Å / Num. unique obs: 5529 / CC1/2: 0.671 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→15 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.769 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.052 / ESU R Free: 0.053 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→15 Å
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Refine LS restraints |
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LS refinement shell |
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