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Open data
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Basic information
Entry | Database: PDB / ID: 6z3n | ||||||
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Title | Apo Structure of a Hydrolase from Pseudomonas aeruginosa PAO1 | ||||||
![]() | Hydrolase | ||||||
![]() | HYDROLASE / Guanosine pentaphosphate phosphohydrolase / small alarmone / ppGpp | ||||||
Function / homology | guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / ACETATE ION / NICKEL (II) ION / Bifunctional (P)ppGpp synthetase/guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jin, Y. / Rizkallah, P. / Bell, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Apo Structure of a Small Alarmone Hydrolase from Pseudomonas aeruginosa PAO1 Authors: Jin, Y. / Rizkallah, P. / Bell, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 301 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 354.4 KB | Display | ![]() |
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Full document | ![]() | 360.4 KB | Display | |
Data in XML | ![]() | 32.6 KB | Display | |
Data in CIF | ![]() | 47.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 23296.412 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA0431 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-NI / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 12 mg/mL of PaSpo2 protein stock in the buffer of 25 mM Tris pH 8.0, 200 mM NaCl, and 10 mM MgCl2 is mixed 1:1 ratio with the precipitant consisted of 4.0 M NH4OAc, 0.1 M Bis-Tris propane, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→59.9 Å / Num. obs: 95945 / % possible obs: 81.3 % / Redundancy: 5.9 % / CC1/2: 0.999 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.58→1.61 Å / Num. unique obs: 1474 / CC1/2: 0.573 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→59.9 Å
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Refine LS restraints |
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LS refinement shell |
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