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Open data
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Basic information
Entry | Database: PDB / ID: 4rnj | ||||||
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Title | PaMorA phosphodiesterase domain, apo form | ||||||
![]() | Motility regulator | ||||||
![]() | HYDROLASE / EAL domain / Phosphodiesterase / c-di-GMP | ||||||
Function / homology | ![]() nucleotide binding / regulation of DNA-templated transcription / identical protein binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Phippen, C.W. / Tews, I. | ||||||
![]() | ![]() Title: Formation and dimerization of the phosphodiesterase active site of the Pseudomonas aeruginosa MorA, a bi-functional c-di-GMP regulator. Authors: Phippen, C.W. / Mikolajek, H. / Schlaefli, H.G. / Keevil, C.W. / Webb, J.S. / Tews, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.7 KB | Display | ![]() |
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PDB format | ![]() | 86.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.8 KB | Display | ![]() |
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Full document | ![]() | 434.4 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 28.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rnfC ![]() 4rnhC ![]() 4rniC ![]() 3n3tS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | Active diguanylate cyclase |
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Components
#1: Protein | Mass: 31727.320 Da / Num. of mol.: 2 / Fragment: EAL domain, UNP residues 1145-1409 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9HVI8, cyclic-guanylate-specific phosphodiesterase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.82 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Imidazole; MES, 0.09M NaN03; Na2HPO4; (NH4)2SO4, 30% Ethylene glycol; PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 14, 2012 |
Radiation | Monochromator: Diamond (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→100 Å / Num. all: 25794 / Num. obs: 25720 / % possible obs: 99.7 % / Redundancy: 4.28 % / Biso Wilson estimate: 42.67 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.87 |
Reflection shell | Resolution: 2.32→2.4 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 1.8 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3N3T Resolution: 2.32→48.741 Å / FOM work R set: 0.8062 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.77 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.79 Å2 / Biso mean: 47.68 Å2 / Biso min: 25.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→48.741 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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