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Yorodumi- PDB-6ggo: Crystal structure of Salmonella zinc metalloprotease effector GtgA -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ggo | |||||||||||||||
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Title | Crystal structure of Salmonella zinc metalloprotease effector GtgA | |||||||||||||||
Components | Bacteriophage virulence determinant | |||||||||||||||
Keywords | METAL BINDING PROTEIN / Protease / Metalloprotease / zinc | |||||||||||||||
Function / homology | PipA / PipA protein / Bacteriophage virulence determinant Function and homology information | |||||||||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||||||||
Authors | Jennings, E. / Esposito, D. / Rittinger, K. / Thurston, T. | |||||||||||||||
Funding support | United Kingdom, 4items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structure-function analyses of the bacterial zinc metalloprotease effector protein GtgA uncover key residues required for deactivating NF-kappa B. Authors: Jennings, E. / Esposito, D. / Rittinger, K. / Thurston, T.L.M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ggo.cif.gz | 236.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ggo.ent.gz | 202.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ggo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ggo_validation.pdf.gz | 433.2 KB | Display | wwPDB validaton report |
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Full document | 6ggo_full_validation.pdf.gz | 433.6 KB | Display | |
Data in XML | 6ggo_validation.xml.gz | 16 KB | Display | |
Data in CIF | 6ggo_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/6ggo ftp://data.pdbj.org/pub/pdb/validation_reports/gg/6ggo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24098.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria) Gene: gtgA, STM14_1166 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A0F6AZI6 #2: Chemical | #3: Chemical | #4: 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: 2.26 Å3/Da / Density % sol: 45.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: GtgA, at a concentration of 24 mg/ml, was crystallyzed in 0.1 M Tris pH 8.5, 25% (v/v) isopropanol and 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→75.3 Å / Num. obs: 13578 / % possible obs: 98.36 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.067 / Rrim(I) all: 0.12 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.6→2.72 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→75.3 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→75.3 Å
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Refine LS restraints |
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LS refinement shell |
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