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Open data
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Basic information
Entry | Database: PDB / ID: 4ml2 | ||||||
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Title | Crystal structure of wild-type YafQ | ||||||
![]() | mRNA interferase YafQ | ||||||
![]() | TOXIN / antitoxin | ||||||
Function / homology | ![]() toxin-antitoxin complex / single-species biofilm formation / regulation of growth / mRNA catabolic process / translational termination / RNA endonuclease activity / RNA endonuclease activity, producing 3'-phosphomonoesters / ribosome binding / Hydrolases; Acting on ester bonds / response to antibiotic ...toxin-antitoxin complex / single-species biofilm formation / regulation of growth / mRNA catabolic process / translational termination / RNA endonuclease activity / RNA endonuclease activity, producing 3'-phosphomonoesters / ribosome binding / Hydrolases; Acting on ester bonds / response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liang, Y.J. / Gao, Z.Q. / Liu, Q.S. / Dong, Y.H. | ||||||
![]() | ![]() Title: Structural and Functional Characterization of Escherichia coli Toxin-Antitoxin Complex DinJ-YafQ Authors: Liang, Y. / Gao, Z. / Wang, F. / Zhang, Y. / Dong, Y. / Liu, Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.5 KB | Display | ![]() |
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PDB format | ![]() | 25.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.5 KB | Display | ![]() |
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Full document | ![]() | 428.6 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 12 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ml0C ![]() 4mmgSC ![]() 4mmjC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11110.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q47149, Hydrolases; Acting on ester bonds | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M (NH4)2SO4, 30% PEG8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 19, 2012 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 22814 / Num. obs: 22754 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 72.5 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 16.3 / Num. unique all: 1104 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MMG Resolution: 1.5→28.79 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 15.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.103 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.5→28.79 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %
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