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Open data
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Basic information
Entry | Database: PDB / ID: 4zvg | ||||||
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Title | Crystal structure of GGDEF domain of the E. coli DosC - form III | ||||||
![]() | Diguanylate cyclase DosC | ||||||
![]() | SIGNALING PROTEIN / oxygen sensing / diguanylate cyclase / cyclic-di-GMP | ||||||
Function / homology | ![]() diguanylate cyclase / negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase activity / carbon monoxide binding / response to oxygen levels / cell adhesion involved in single-species biofilm formation / oxygen binding / heme binding / GTP binding / protein homodimerization activity ...diguanylate cyclase / negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase activity / carbon monoxide binding / response to oxygen levels / cell adhesion involved in single-species biofilm formation / oxygen binding / heme binding / GTP binding / protein homodimerization activity / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tarnawski, M. / Barends, T.R.M. / Schlichting, I. | ||||||
![]() | ![]() Title: Structural analysis of an oxygen-regulated diguanylate cyclase. Authors: Tarnawski, M. / Barends, T.R. / Schlichting, 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 | ![]() | 79.2 KB | Display | ![]() |
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PDB format | ![]() | 59.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.5 KB | Display | ![]() |
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Full document | ![]() | 437.3 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zvaC ![]() 4zvbC ![]() 4zvcC ![]() 4zvdC ![]() 4zveSC ![]() 4zvfC ![]() 4zvhC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19900.594 Da / Num. of mol.: 2 / Fragment: UNP residues 297-460 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.2M potassium sodium tartrate, 22% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97627 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 18580 / % possible obs: 97.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.36 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 2.54 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZVE Resolution: 2.2→48.61 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.22 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→48.61 Å
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Refine LS restraints |
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LS refinement shell |
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