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Yorodumi- PDB-6z3o: The E74Q mutant of Small Alarmone Hydrolase SAH from Pseudomonas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z3o | ||||||
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Title | The E74Q mutant of Small Alarmone Hydrolase SAH from Pseudomonas aeruginosa PAO1 | ||||||
Components | Small Alarmone Hydrolase | ||||||
Keywords | HYDROLASE / Guanosine pentaphosphate phosphohydrolase / small alarmone / ppGpp | ||||||
Function / homology | guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / : / Bifunctional (P)ppGpp synthetase/guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Jin, Y. / Rizkallah, P. / Bell, H. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z3o.cif.gz | 302.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z3o.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6z3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/6z3o ftp://data.pdbj.org/pub/pdb/validation_reports/z3/6z3o | HTTPS FTP |
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-Related structure data
Related structure data | 6z3nSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23107.846 Da / Num. of mol.: 4 / Mutation: E74Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0431 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I686 #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 14.6 mg/mL of PaSpo2 E74Q variant protein stock in the buffer of 25 mM Tris pH 8.0, 200 mM NaCl, 10 mM ppGpp and 10 mM MnCl2 is mixed 1:1 ratio with the precipitant consisted of 4.0 M ...Details: 14.6 mg/mL of PaSpo2 E74Q variant protein stock in the buffer of 25 mM Tris pH 8.0, 200 mM NaCl, 10 mM ppGpp and 10 mM MnCl2 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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
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: 1.74→57.28 Å / Num. obs: 89102 / % possible obs: 89.6 % / Redundancy: 3.8 % / CC1/2: 0.994 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.74→1.77 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4525 / CC1/2: 0.422 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Z3N Resolution: 1.74→43.062 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.306 / SU ML: 0.109 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.11 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: 29.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→43.062 Å
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Refine LS restraints |
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LS refinement shell |
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