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Yorodumi- PDB-4y9o: PA3825-EAL Metal-Free-Apo Structure - Manganese Co-crystallisation -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y9o | |||||||||
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Title | PA3825-EAL Metal-Free-Apo Structure - Manganese Co-crystallisation | |||||||||
Components | PA3825-EAL | |||||||||
Keywords | UNKNOWN FUNCTION / EAL / Cyclic di-GMP | |||||||||
Function / homology | Function and homology information cyclic-guanylate-specific phosphodiesterase / cyclic-guanylate-specific phosphodiesterase activity / nucleotide binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | |||||||||
Authors | Bellini, D. / Horrell, S. / Wagner, A. / Strange, R. / Walsh, M.A. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: MucR and PA3825 EAL-phosphodiesterase domains from Pseudomonas aeruginosa suggest roles for three metals in the active site Authors: Bellini, D. / Horrell, S. / Wagner, A. / Strange, R. / Hutchin, A. / Webb, J.S. / Tews, I. / Walsh, M.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y9o.cif.gz | 120 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y9o.ent.gz | 93.7 KB | Display | PDB format |
PDBx/mmJSON format | 4y9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/4y9o ftp://data.pdbj.org/pub/pdb/validation_reports/y9/4y9o | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29197.307 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA3825 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HXH7 |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.8 M sodium phosphate monobasic, 1.2 M potassium phosphate dibasic and 0.1 M sodium acetate pH 4.5, 0.2 M Manganese Chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.77 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.77 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→58.15 Å / Num. all: 26471 / Num. obs: 25106 / % possible obs: 99.09 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.81→1.857 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.4 / % possible all: 91.71 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→58.15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.47 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→58.15 Å
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Refine LS restraints |
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