+
Open data
-
Basic information
Entry | Database: PDB / ID: 5cke | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | E.coli MazF E24A form IIa | |||||||||
![]() | Endoribonuclease MazF | |||||||||
![]() | HYDROLASE / Toxin-Antitoxin / mRNA interferase / ribonuclease / persistence / bacterial stress response | |||||||||
Function / homology | ![]() 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 ...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 / defense response to virus / protein-containing complex binding / regulation of DNA-templated transcription / protein homodimerization activity / protein-containing complex / DNA binding / RNA binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zorzini, V. / Loris, R. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 93.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 71 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 476.7 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ck9C ![]() 5ckbC ![]() 5ckdC ![]() 5ckfC ![]() 5ckhC ![]() 5co7C ![]() 5cqxC ![]() 5cqyC ![]() 5cr2C ![]() 1ub4S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 13083.104 Da / Num. of mol.: 2 / Mutation: E24A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: mazF, chpA, chpAK, b2782, JW2753 / Production host: ![]() ![]() References: UniProt: P0AE70, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters #2: Chemical | ChemComp-SO4 / | #3: Chemical | ChemComp-MRD / ( | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 48.16 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.1 MES pH 6.2, 1.6M Ammonium Sulfate, 10% (v/v) 1,4-dioxane |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8081 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→33.9 Å / Num. obs: 11801 / % possible obs: 96.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 36.65 Å2 / Rsym value: 0.115 / Net I/σ(I): 12.9 |
Reflection shell | Highest resolution: 2.3 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1377 / Rsym value: 0.742 / % possible all: 97.6 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1UB4 Resolution: 2.311→31.327 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.37 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.824 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.311→31.327 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|