+
Open data
-
Basic information
Entry | Database: PDB / ID: 7v9z | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | PaOrn Oligoribonuclease native structure | |||||||||
![]() | Oligoribonuclease | |||||||||
![]() | HYDROLASE / PaOrn / Oligoribonuclease / Pseudomonas aeruginosa. | |||||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / nucleic acid metabolic process / 3'-5'-RNA exonuclease activity / nucleic acid binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, J. / Zhang, Q. / Bartlam, M. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: PaOrn Oligoribonuclease native structure Authors: Zhang, J. / Zhang, Q. / Bartlam, M. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 205.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 135.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 888.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 889.3 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ytaS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 20853.596 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: orn, PA4951 / Production host: ![]() ![]() References: UniProt: P57665, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-IMD / | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.96 Å3/Da / Density % sol: 68.9 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 1.0M (NH4)2HPO4, 0.1M imidazole pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 54666 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 28.84 Å2 / Rpim(I) all: 0.047 / Net I/σ(I): 21.06 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.27 / Num. unique obs: 2732 / Rpim(I) all: 0.462 / % possible all: 99.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1YTA Resolution: 1.85→37.22 Å / SU ML: 0.1942 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.8127 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→37.22 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 7.05824318902 Å / Origin y: 14.6615007002 Å / Origin z: 0.0187184320311 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |