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Open data
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Basic information
Entry | Database: PDB / ID: 6uhp | |||||||||
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Title | Crystal Structure of C148 mGFP-ncDNA-1 | |||||||||
![]() | C148 mGFP-ncDNA-1 | |||||||||
![]() | 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 | ![]() | 100.8 KB | Display | ![]() |
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PDB format | ![]() | 73.1 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 ![]() 6uhqC ![]() 6uhrC ![]() 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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1 | ![]()
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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.) ![]() ![]() ![]() ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.82 % / Description: Green needles |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 1 microliter C148 mGFP-ncDNA-1 (5 mg/mL (protein concentration) in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (0.2 M sodium chloride, 0.1 M Bis-Tris ...Details: 1 microliter C148 mGFP-ncDNA-1 (5 mg/mL (protein concentration) in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (0.2 M sodium chloride, 0.1 M Bis-Tris Buffer pH 5.5, 25% (w/v) PEG 3350) in a sitting drop with a 70 microliter reservoir (0.2 M sodium chloride, 0.1 M Bis-Tris Buffer pH 5.5, 25% (w/v) PEG 3350) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 3, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.9→96.037 Å / Num. all: 13070 / Num. obs: 13070 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rpim(I) all: 0.073 / Rrim(I) all: 0.165 / Rsym value: 0.147 / Net I/av σ(I): 2.8 / Net I/σ(I): 7.9 / Num. measured all: 66203 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5N9O Resolution: 2.9→56.48 Å / Cor.coef. Fo:Fc: 0.623 / Cor.coef. Fo:Fc free: 0.489 / WRfactor Rfree: 0.323 / WRfactor Rwork: 0.2922 / FOM work R set: 0.5981 / SU B: 24.706 / SU ML: 0.506 / SU R Cruickshank DPI: 0.1106 / SU Rfree: 0.1214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.121 / 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: 158.79 Å2 / Biso mean: 55.365 Å2 / Biso min: 4.87 Å2
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Refinement step | Cycle: final / Resolution: 2.9→56.48 Å
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LS refinement shell | Resolution: 2.904→2.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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