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- PDB-6gfm: Crystal structure of the Escherichia coli nucleosidase PpnN (pppG... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gfm | |||||||||
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Title | Crystal structure of the Escherichia coli nucleosidase PpnN (pppGpp-form) | |||||||||
![]() | Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase | |||||||||
![]() | ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, Y. / Baerentsen, R.L. / Gerdes, K. / Brodersen, D.E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: (p)ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch. Authors: Zhang, Y.E. / Baerentsen, R.L. / Fuhrer, T. / Sauer, U. / Gerdes, K. / Brodersen, D.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 198 KB | Display | ![]() |
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PDB format | ![]() | 156.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6gflSC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 53244.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P0ADR8, ![]() ![]() ![]() |
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#2: Chemical | ChemComp-0O2 / |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.64 % |
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Crystal grow![]() | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.4M KNa tartrate hydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.77→34.7 Å / Num. obs: 19332 / % possible obs: 99.77 % / Redundancy: 24.8 % / Biso Wilson estimate: 84.07 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1421 / Rpim(I) all: 0.029 / Rrim(I) all: 0.1451 / Net I/σ(I): 17.45 |
Reflection shell | Resolution: 2.77→2.869 Å / Redundancy: 18.2 % / Rmerge(I) obs: 2.704 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 1907 / CC1/2: 0.58 / Rpim(I) all: 0.6416 / Rrim(I) all: 2.781 / % possible all: 99.74 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6GFL Resolution: 2.77→34.7 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.77→34.7 Å
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