+Open data
-Basic information
Entry | Database: PDB / ID: 6zqo | ||||||
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Title | EYFP mutant - F165G | ||||||
Components | G protein/GFP fusion protein | ||||||
Keywords | FLUORESCENT PROTEIN / Alternative routes of post-translation chemistry | ||||||
Function / homology | Function and homology information bioluminescence / generation of precursor metabolites and energy / symbiont entry into host cell / viral envelope / virion attachment to host cell / membrane Similarity search - Function | ||||||
Biological species | Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Pletnev, V.Z. / Pletnev, S.V. / Pletneva, N.V. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Comput Struct Biotechnol J / Year: 2021 Title: Amino acid residue at the 165th position tunes EYFP chromophore maturation. A structure-based design. Authors: Pletneva, N.V. / Maksimov, E.G. / Protasova, E.A. / Mamontova, A.V. / Simonyan, T.R. / Ziganshin, R.H. / Lukyanov, K.A. / Muslinkina, L. / Pletnev, S. / Bogdanov, A.M. / Pletnev, V.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zqo.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zqo.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 6zqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zqo_validation.pdf.gz | 327.2 KB | Display | wwPDB validaton report |
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Full document | 6zqo_full_validation.pdf.gz | 330.3 KB | Display | |
Data in XML | 6zqo_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 6zqo_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/6zqo ftp://data.pdbj.org/pub/pdb/validation_reports/zq/6zqo | HTTPS FTP |
-Related structure data
Related structure data | 1yfpS 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: 28321.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP Gene: G, GFP / Production host: Escherichia coli (E. coli) / References: UniProt: B7UCZ6 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 5.7 mg/ml in 20mM Tris 8.0 200 mM NaCl mixed with a 1.44M (NH4)2SO4, 60mM Bicine pH 9.0 reservoir solution. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 3, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→30 Å / Num. obs: 14573 / % possible obs: 94.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.028 / Rrim(I) all: 0.066 / Χ2: 0.816 / Net I/σ(I): 9.8 / Num. measured all: 83201 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YFP Resolution: 2.2→29.4 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.895 / SU B: 13.277 / SU ML: 0.306 / SU R Cruickshank DPI: 0.3214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.287 / 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: 138.06 Å2 / Biso mean: 64.924 Å2 / Biso min: 32.57 Å2
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Refinement step | Cycle: final / Resolution: 2.2→29.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.202→2.259 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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