+Open data
-Basic information
Entry | Database: PDB / ID: 4k59 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Pseudomonas Aeruginosa RsmF | ||||||
Components | RNA BINDING PROTEIN RsmF | ||||||
Keywords | RNA BINDING PROTEIN / beta sandwich | ||||||
Function / homology | Function and homology information regulation of carbohydrate metabolic process / mRNA catabolic process / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å | ||||||
Authors | Betts, L. / Walton, W.G. / Redinbo, M.R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: An unusual CsrA family member operates in series with RsmA to amplify posttranscriptional responses in Pseudomonas aeruginosa. Authors: Marden, J.N. / Diaz, M.R. / Walton, W.G. / Gode, C.J. / Betts, L. / Urbanowski, M.L. / Redinbo, M.R. / Yahr, T.L. / Wolfgang, M.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4k59.cif.gz | 36 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4k59.ent.gz | 24.9 KB | Display | PDB format |
PDBx/mmJSON format | 4k59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k59_validation.pdf.gz | 422.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4k59_full_validation.pdf.gz | 423.2 KB | Display | |
Data in XML | 4k59_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 4k59_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/4k59 ftp://data.pdbj.org/pub/pdb/validation_reports/k5/4k59 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 8067.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: UCBPP-PA14 / Gene: PA14_68470 / Plasmid: pMCSG-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: Q02EI1, UniProt: A0A0H2ZIZ8*PLUS |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.96 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.5 Details: 30% PEG 4000, 0.2 M Magnesium chloride, 0.1 M Tris-HCl, pH 8.5, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2012 / Details: Confocal optics | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Confocal optic / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.22→50 Å / Num. obs: 3743 / % possible obs: 98.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 42.83 Å2 / Rmerge(I) obs: 0.049 / Χ2: 1.468 / Net I/σ(I): 16.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→32.302 Å / Occupancy max: 1 / Occupancy min: 0.7 / FOM work R set: 0.711 / SU ML: 0.27 / σ(F): 1.37 / Phase error: 34.01 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.22 Å2 / Biso mean: 62.6779 Å2 / Biso min: 27.06 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.22→32.302 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
|