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Open data
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Basic information
Entry | Database: PDB / ID: 6uhr | |||||||||
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Title | Crystal Structure of C148 mGFP-scDNA-2 | |||||||||
![]() | C148 mGFP-scDNA-2 | |||||||||
![]() | FLUORESCENT PROTEIN / green fluorescent protein / beta-barrel / DNA / protein-DNA conjugate | |||||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Winegar, P.W. / Hayes, O.G. / McMillan, J.R. / Figg, C.A. / Focia, P.J. / Mirkin, C.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: DNA-Directed Protein Packing within Single Crystals. Authors: Winegar, P.H. / Hayes, O.G. / McMillan, J.R. / Figg, C.A. / Focia, P.J. / Mirkin, C.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.9 KB | Display | ![]() |
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PDB format | ![]() | 74.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6uhjC ![]() 6uhkC ![]() 6uhlC ![]() 6uhmC ![]() 6uhnC ![]() 6uhoC ![]() 6uhpC ![]() 6uhqC ![]() 5n9oS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31038.908 Da / Num. of mol.: 2 / Mutation: S148C Source method: isolated from a genetically manipulated source Details: This mutant of EGFP has a single surface cysteine at residue 148 (counting from M37 and counting CRO as 3 residues) and an N-terminal his-tag. Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.28 % / Description: Green crystals with sharp facets |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 1 microliter C148 mGFP-scDNA-2 (5 mg/mL (protein concentration) in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (0.15 M potassium bromide, 30% (w/v) PEG ...Details: 1 microliter C148 mGFP-scDNA-2 (5 mg/mL (protein concentration) in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (0.15 M potassium bromide, 30% (w/v) PEG 2000 MME) in a sitting drop with a 70 microliter reservoir (0.15 M potassium bromide, 30% (w/v) PEG 2000 MME) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 18, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→104.595 Å / Num. all: 11425 / Num. obs: 11425 / % possible obs: 99.7 % / Redundancy: 6.9 % / Rpim(I) all: 0.078 / Rrim(I) all: 0.21 / Rsym value: 0.194 / Net I/av σ(I): 3.6 / Net I/σ(I): 8 / Num. measured all: 79211 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5N9O Resolution: 3→52.35 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.822 / WRfactor Rfree: 0.2741 / WRfactor Rwork: 0.2 / FOM work R set: 0.7777 / SU B: 16.846 / SU ML: 0.337 / SU Rfree: 0.5275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.528 / 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: 98.65 Å2 / Biso mean: 41.072 Å2 / Biso min: 15.22 Å2
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Refinement step | Cycle: final / Resolution: 3→52.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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