+Open data
-Basic information
Entry | Database: PDB / ID: 6qmn | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a Ribonuclease A-Onconase chimera | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | HYDROLASE / pancreatic ribonuclease A / alpha/beta fold / chimera | ||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Bison bison (American bison) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Esposito, L. / Vitagliano, L. / Ruggiero, A. / Picone, D. / Leone, S. / Donnarumma, F. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2019 Title: Structure, stability and aggregation propensity of a Ribonuclease A-Onconase chimera. Authors: Esposito, L. / Donnarumma, F. / Ruggiero, A. / Leone, S. / Vitagliano, L. / Picone, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6qmn.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6qmn.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 6qmn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qmn_validation.pdf.gz | 455.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6qmn_full_validation.pdf.gz | 460.3 KB | Display | |
Data in XML | 6qmn_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 6qmn_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/6qmn ftp://data.pdbj.org/pub/pdb/validation_reports/qm/6qmn | HTTPS FTP |
-Related structure data
Related structure data | 1kf4S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13491.060 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bison bison (American bison) / Gene: RNASE1, RNS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61824, EC: 3.1.27.5 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.17 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 0.100 M Bis-Tris pH 6.5, 28 % W/V Polyethylene glycol monomethyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5419 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→28 Å / Num. obs: 16885 / % possible obs: 96.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.31→2.38 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1664 / % possible all: 96.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1kf4 Resolution: 2.31→27.85 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.871 / SU B: 12.029 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.421 / ESU R Free: 0.303 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.21 Å2 / Biso mean: 46.698 Å2 / Biso min: 23.81 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.31→27.85 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.309→2.369 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|