+Open data
-Basic information
Entry | Database: PDB / ID: 4mml | ||||||
---|---|---|---|---|---|---|---|
Title | D40A Hfq from Pseudomonas aeruginosa | ||||||
Components | Protein hfq | ||||||
Keywords | RNA BINDING PROTEIN / LSM fold | ||||||
Function / homology | Function and homology information regulation of translation, ncRNA-mediated / regulation of carbon utilization / regulation of RNA stability / quorum sensing / regulation of translation / regulation of DNA-templated transcription / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å | ||||||
Authors | Murina, V.N. / Filimonov, V.V. / Melnik, B.S. / Uhlein, M. / Mueller, U. / Weiss, M. / Nikulin, A.D. | ||||||
Citation | Journal: Biochemistry Mosc. / Year: 2014 Title: Effect of conserved intersubunit amino Acid substitutions on hfq protein structure and stability. Authors: Murina, V.N. / Melnik, B.S. / Filimonov, V.V. / Uhlein, M. / Weiss, M.S. / Muller, U. / Nikulin, A.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4mml.cif.gz | 27.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4mml.ent.gz | 17.1 KB | Display | PDB format |
PDBx/mmJSON format | 4mml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/4mml ftp://data.pdbj.org/pub/pdb/validation_reports/mm/4mml | HTTPS FTP |
---|
-Related structure data
Related structure data | 4mmkC 1u1sS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 6||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 9070.478 Da / Num. of mol.: 1 / Mutation: D40A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: hfq, PA4944 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HUM0 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-U / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.52 % |
---|---|
Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 7% w/v PEG2000 MME, 2% MPD, 20 micromolar zinc chloride, 50 mM Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 2009 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→35 Å / Num. all: 6611 / Num. obs: 6611 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 3.1 / % possible all: 99 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1U1S Resolution: 1.801→32.895 Å / Isotropic thermal model: ISOTROPIC / σ(F): 1.34 / Phase error: 30.38 / Stereochemistry target values: TWIN_LSQ_F
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.9 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.801→32.895 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|