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- PDB-6pdk: The Structure of Smlt3025, an immunity protein of the Stenotropho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pdk | |||||||||
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Title | The Structure of Smlt3025, an immunity protein of the Stenotrophomonas maltophilia type IV secretion system | |||||||||
![]() | Uncharacterized protein | |||||||||
![]() | ANTITOXIN / Type IV Secretion System / Bacterial competition | |||||||||
Function / homology | BROMIDE ION / Uncharacterized protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Matsuyama, B.Y. / Farah, C.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The opportunistic pathogen Stenotrophomonas maltophilia utilizes a type IV secretion system for interbacterial killing. Authors: Bayer-Santos, E. / Cenens, W. / Matsuyama, B.Y. / Oka, G.U. / Di Sessa, G. / Mininel, I.D.V. / Alves, T.L. / Farah, C.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.8 KB | Display | ![]() |
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PDB format | ![]() | 49.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.9 KB | Display | ![]() |
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Full document | ![]() | 436.6 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 30486.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: K279a / Gene: Smlt3025 / Plasmid: pET28a / Production host: ![]() ![]() | ||||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-BR / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Imidazole/MES Monohydrate pH 6.5 0.03M Sodium Fluoride 0.03M Sodium Bromide 0.03M Sodium Iodide 12.5% MPD 12.5% PEG10000 12.5% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.05 Å / Num. obs: 19897 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 33.03 Å2 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.9→1.91 Å / Num. unique obs: 3140 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→21.87 Å
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Refine LS restraints |
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LS refinement shell |
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