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Yorodumi- PDB-5cqx: E. coli MazF mutant E24A in complex with MazE residues 68-82 form I -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cqx | |||||||||
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Title | E. coli MazF mutant E24A in complex with MazE residues 68-82 form I | |||||||||
Components |
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Keywords | HYDROLASE / Toxin-Antitoxin / mRNA interferase / ribonuclease / persistence / bacterial stress response | |||||||||
Function / homology | Function and homology information toxin sequestering activity / toxin-antitoxin complex / quorum sensing / rRNA catabolic process / single-species biofilm formation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / positive regulation of programmed cell death / regulation of growth / mRNA catabolic process / RNA endonuclease activity ...toxin sequestering activity / toxin-antitoxin complex / quorum sensing / rRNA catabolic process / single-species biofilm formation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / positive regulation of programmed cell death / regulation of growth / mRNA catabolic process / RNA endonuclease activity / molecular function activator activity / negative regulation of cell growth / regulation of translation / double-stranded DNA binding / defense response to virus / regulation of DNA-templated transcription / protein-containing complex binding / protein homodimerization activity / protein-containing complex / DNA binding / RNA binding Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | |||||||||
Authors | Zorzini, V. / Loris, R. | |||||||||
Funding support | Belgium, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Substrate Recognition and Activity Regulation of the Escherichia coli mRNA Endonuclease MazF. Authors: Zorzini, V. / Mernik, A. / Lah, J. / Sterckx, Y.G. / De Jonge, N. / Garcia-Pino, A. / De Greve, H. / Versees, W. / Loris, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cqx.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cqx.ent.gz | 84.2 KB | Display | PDB format |
PDBx/mmJSON format | 5cqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/5cqx ftp://data.pdbj.org/pub/pdb/validation_reports/cq/5cqx | HTTPS FTP |
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-Related structure data
Related structure data | 5ck9C 5ckbC 5ckdC 5ckeC 5ckfC 5ckhC 5co7C 5cqyC 5cr2C 1ub4S 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: 13083.104 Da / Num. of mol.: 2 / Mutation: E24A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mazF, chpA, chpAK, b2782, JW2753 / Production host: Escherichia coli (E. coli) References: UniProt: P0AE70, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: Protein/peptide | | Mass: 1885.016 Da / Num. of mol.: 1 / Fragment: UNP residues 68-82 / Source method: obtained synthetically / Details: Peptide / Source: (synth.) Escherichia coli K-12 (bacteria) / References: UniProt: P0AE72 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density % sol: 27.2 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Magnesium Chloride, 0.1M Sodium Cacodylate pH6.5, 50% v/v PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→42.74 Å / Num. obs: 22847 / % possible obs: 95.9 % / Redundancy: 3.62 % / Rsym value: 0.1 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.63→1.73 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.11 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UB4 Resolution: 1.63→42.745 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.416 Å2 / ksol: 0.393 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.63→42.745 Å
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Refine LS restraints |
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LS refinement shell |
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