[English] 日本語
Yorodumi- PDB-4j40: Crystal structure of the dual-domain GGDEF-EAL module of FimX fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j40 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the dual-domain GGDEF-EAL module of FimX from Pseudomonas aeruginosa | |||||||||
Components | FimX | |||||||||
Keywords | HYDROLASE / EAL PHOSPHODIESTERASE / BIOFILM / C-DI-GMP EFFECTOR / C-DI-GMP | |||||||||
Function / homology | Function and homology information phosphorelay signal transduction system / nucleotide binding / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.99 Å | |||||||||
Authors | Navarro, M.V. / De, N. / Bae, N. / Wang, Q. / Sondermann, H. | |||||||||
Citation | Journal: Structure / Year: 2009 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. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4j40.cif.gz | 111.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4j40.ent.gz | 85 KB | Display | PDB format |
PDBx/mmJSON format | 4j40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/4j40 ftp://data.pdbj.org/pub/pdb/validation_reports/j4/4j40 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 47749.980 Da / Num. of mol.: 2 / Fragment: GGDEF and EAL domains: UNP residues 260-691 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: fimX, PA4959 / Plasmid: ppSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9HUK6, cyclic-guanylate-specific phosphodiesterase |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.95 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Na formate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9771 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 2, 2007 |
Radiation | Monochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9771 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→48.9 Å / Num. obs: 20711 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Rmerge(I) obs: 0.062 |
Reflection shell | Resolution: 2.99→3.18 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 4.4 / Num. unique all: 6702 / % possible all: 97.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.99→25.363 Å / SU ML: 0.37 / σ(F): 2 / Phase error: 24.95 / Stereochemistry target values: MLHL
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.99→25.363 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|