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Open data
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Basic information
Entry | Database: PDB / ID: 3hv9 | ||||||
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Title | Crystal structure of FimX EAL domain from Pseudomonas aeruginosa | ||||||
![]() | Protein FimX | ||||||
![]() | HYDROLASE / EAL phosphodiesterase / biofilm / c-di-GMP | ||||||
Function / homology | ![]() phosphorelay signal transduction system / nucleotide binding / regulation of DNA-templated transcription / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Navarro, M.V.A.S. / De, N. / Bae, N. / Sondermann, H. | ||||||
![]() | ![]() Title: Structural analysis of the GGDEF-EAL domain-containing c-di-GMP receptor FimX. Authors: Navarro, M.V. / De, N. / Bae, N. / Wang, Q. / Sondermann, H. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.7 KB | Display | ![]() |
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PDB format | ![]() | 49.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.3 KB | Display | ![]() |
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Full document | ![]() | 452.2 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hv8C ![]() 3hvaC ![]() 4j40C ![]() 3hvb 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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Components
#1: Protein | Mass: 29061.959 Da / Num. of mol.: 1 / Fragment: EAL domain: UNP residues 429-691 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9HUK6, cyclic-guanylate-specific phosphodiesterase | ||
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#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: Ammonium sulfate, PEG 8000, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2008 |
Radiation | Monochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.298→46.732 Å / Num. all: 20760 / Num. obs: 20719 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 31.7 |
Reflection shell | Resolution: 2.298→2.43 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 4.4 / Num. unique all: 6702 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3HVB ![]() 3hvb Resolution: 2.298→46.722 Å / SU ML: 0.3 / σ(F): 1.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.751 Å2 / ksol: 0.369 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.298→46.722 Å
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Refine LS restraints |
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LS refinement shell |
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