+Open data
-Basic information
Entry | Database: PDB / ID: 5dlo | ||||||
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Title | S. aureus MazF in complex with substrate analogue | ||||||
Components |
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Keywords | HYDROLASE / Toxin-Antitoxin / mRNA interferase / ribonuclease / persistence / bacterial stress response | ||||||
Function / homology | Function and homology information rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) Enterobacterio phage MS2 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å | ||||||
Authors | Zorzini, V. / Loris, R. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: To Be Published Title: Substrate recognition, regulation mechanism and activity regulation of MazF mRNA interferase. Authors: Zorzini, V. / Loris, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dlo.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dlo.ent.gz | 54.9 KB | Display | PDB format |
PDBx/mmJSON format | 5dlo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/5dlo ftp://data.pdbj.org/pub/pdb/validation_reports/dl/5dlo | HTTPS FTP |
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-Related structure data
Related structure data | 4mzmS S: Starting model for refinement |
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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
#1: Protein | Mass: 14952.206 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mazF, SAHV_2053 / Production host: Escherichia coli (E. coli) References: UniProt: A7X4P5, UniProt: Q2FWI8*PLUS, Hydrolases; Acting on ester bonds |
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#2: DNA chain | Mass: 2077.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacterio phage MS2 (virus) |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.43 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 75 mM Tris pH 8.5, 18.75% v/v tert-Butanol, 25% Glycerol |
-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: Nov 15, 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: 1.4→31.8 Å / Num. obs: 31425 / % possible obs: 99 % / Redundancy: 5.4 % / Rsym value: 0.048 / Net I/σ(I): 21.64 |
Reflection shell | Resolution: 1.4→1.49 Å / Mean I/σ(I) obs: 2.03 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MZM Resolution: 1.401→31.8 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 14.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.992 Å2 / ksol: 0.416 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.401→31.8 Å
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Refine LS restraints |
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LS refinement shell |
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