+Open data
-Basic information
Entry | Database: PDB / ID: 4mmj | ||||||
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Title | crystal structure of YafQ from E.coli strain BL21(DE3) | ||||||
Components | Addiction module toxin, RelE/StbE family | ||||||
Keywords | TOXIN / antitoxin | ||||||
Function / homology | Function and homology information endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli BL21 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Liang, Y. / Gao, Z. / Liu, Q. / Dong, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mmj.cif.gz | 35.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mmj.ent.gz | 23.5 KB | Display | PDB format |
PDBx/mmJSON format | 4mmj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/4mmj ftp://data.pdbj.org/pub/pdb/validation_reports/mm/4mmj | HTTPS FTP |
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-Related structure data
Related structure data | 4ml0C 4ml2C 4mmgSC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11114.878 Da / Num. of mol.: 1 / Mutation: H87Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) / Gene: yafQ / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: C6EA63, UniProt: A0A140NAP5*PLUS | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M (NH4)2SO4, 30%PEG8000, 10mM Pr(Ac)3, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9792 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 9, 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: 1.8→50 Å / Num. all: 12628 / Num. obs: 12280 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 49.1 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 7 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 10.2 / Num. unique all: 622 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MMG Resolution: 1.8→38.001 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 26.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→38.001 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: 4
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