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Open data
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Basic information
Entry | Database: PDB / ID: 6uhl | |||||||||
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Title | Crystal Structure of C148 mGFP-scDNA-1 | |||||||||
![]() | C148 mGFP-scDNA-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 / Unknown ligand / 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 | ![]() | 111.1 KB | Display | ![]() |
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PDB format | ![]() | 81.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.3 KB | Display | ![]() |
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Full document | ![]() | 441 KB | Display | |
Data in XML | ![]() | 22.8 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6uhjC ![]() 6uhkC ![]() 6uhmC ![]() 6uhnC ![]() 6uhoC ![]() 6uhpC ![]() 6uhqC ![]() 6uhrC ![]() 4eulS 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.) ![]() ![]() ![]() ![]() #2: Chemical | Mass: 32.065 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: 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: 2.37 Å3/Da / Density % sol: 48 % / Description: Crystal was a thin green plate |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 1 microliter C148 mGFP-scDNA-1 (5 mg/mL (protein concentration) in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (0.1 M SPG Buffer pH 8, 25% (w/v) PEG 1500) ...Details: 1 microliter C148 mGFP-scDNA-1 (5 mg/mL (protein concentration) in 10 mM Tris Buffer pH 7.4, 137 mM NaCl) + 1 microliter crystallization condition (0.1 M SPG Buffer pH 8, 25% (w/v) PEG 1500) in a sitting drop with a 70 microliter reservoir (0.1 M SPG Buffer pH 8, 25% (w/v) PEG 1500) PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 3, 2018 | |||||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.91→43.29 Å / Num. obs: 43945 / % possible obs: 96.9 % / Redundancy: 9.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.04 / Rrim(I) all: 0.128 / Net I/σ(I): 12.1 / Num. measured all: 435564 / Scaling rejects: 6 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4EUL Resolution: 1.91→43.29 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.2603 / WRfactor Rwork: 0.2151 / FOM work R set: 0.7617 / SU B: 4.698 / SU ML: 0.133 / SU R Cruickshank DPI: 0.1704 / SU Rfree: 0.1623 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.162 / 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: 122.45 Å2 / Biso mean: 19.491 Å2 / Biso min: 1.39 Å2
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Refinement step | Cycle: final / Resolution: 1.91→43.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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