+Open data
-Basic information
Entry | Database: PDB / ID: 7ym7 | |||||||||
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Title | Crystal structure of the Salmonella effector SseK1 F187A mutant | |||||||||
Components | Type III secretion system effector arginine glycosyltransferase SseK1 | |||||||||
Keywords | TOXIN / salmonella / effector / arginine glycosylation | |||||||||
Function / homology | transferase activity / Type III secretion system effector arginine glycosyltransferase SseK1 Function and homology information | |||||||||
Biological species | Salmonella enterica (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | |||||||||
Authors | Kim, U.J. / Park, J.B. / Yoo, Y. / Cho, H.S. | |||||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Sci Rep / Year: 2022 Title: Catalytic DxD motif caged in Asx-turn and Met-aromatic interaction attenuates the pathogenic glycosylation of SseK2/NleB2 effectors. Authors: Koh, E. / Kim, U. / Cho, H.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ym7.cif.gz | 131.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ym7.ent.gz | 100.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ym7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ym7_validation.pdf.gz | 439.5 KB | Display | wwPDB validaton report |
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Full document | 7ym7_full_validation.pdf.gz | 452 KB | Display | |
Data in XML | 7ym7_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 7ym7_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/7ym7 ftp://data.pdbj.org/pub/pdb/validation_reports/ym/7ym7 | HTTPS FTP |
-Related structure data
Related structure data | 7ym5C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35107.641 Da / Num. of mol.: 2 / Mutation: F187A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: G3V45_004211, G4O83_004375, G4X61_004300 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A735ZBM9 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.98 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium Sulfate 0.1 M MES:NaOH pH 6.5 30% (w/v) PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→46.09 Å / Num. obs: 34504 / % possible obs: 98.73 % / Redundancy: 5.2 % / Biso Wilson estimate: 49.68 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06397 / Rpim(I) all: 0.03048 / Rrim(I) all: 0.07112 / Net I/σ(I): 15.03 |
Reflection shell | Resolution: 2.2→2.279 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.265 / Mean I/σ(I) obs: 1.33 / Num. unique obs: 3381 / CC1/2: 0.819 / CC star: 0.949 / Rpim(I) all: 0.577 / Rrim(I) all: 0.07112 / % possible all: 97.77 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→46.09 Å / SU ML: 0.3928 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.4251 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→46.09 Å
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Refine LS restraints |
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LS refinement shell |
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