+Open data
-Basic information
Entry | Database: PDB / ID: 5kdg | ||||||
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Title | Crystal Structure of Salmonella Typhimurium Effector GtgE | ||||||
Components | Gifsy-2 prophage protein | ||||||
Keywords | HYDROLASE / papain-like fold / cysteine protease / virulence factor / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / PSI-Biology | ||||||
Function / homology | Gifsy-2 prophage protein Function and homology information | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Kozlov, G. / Xu, C. / Wong, K. / Gehring, K. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Funding support | Canada, 1items
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Citation | Journal: PLoS ONE / Year: 2016 Title: Crystal Structure of the Salmonella Typhimurium Effector GtgE. Authors: Xu, C. / Kozlov, G. / Wong, K. / Gehring, K. / Cygler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kdg.cif.gz | 93.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kdg.ent.gz | 70.1 KB | Display | PDB format |
PDBx/mmJSON format | 5kdg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kdg_validation.pdf.gz | 452.4 KB | Display | wwPDB validaton report |
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Full document | 5kdg_full_validation.pdf.gz | 454.7 KB | Display | |
Data in XML | 5kdg_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 5kdg_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/5kdg ftp://data.pdbj.org/pub/pdb/validation_reports/kd/5kdg | HTTPS FTP |
-Related structure data
Related structure data | 4mi7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Monomer as determined by size-exclusion chromatography |
-Components
#1: Protein | Mass: 22889.432 Da / Num. of mol.: 1 / Fragment: residues 17-217 / Mutation: C45S, D123N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) Gene: SBOV09681, DD95_21385, ERS450001_01848, SEETMRM9437_5135, TJ44_09000 Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9XC73, papain | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.8 M ammonium sulfate, 0.1 M Bis-Tris (pH 5.5) and 20% (w/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6362 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6362 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→57.1 Å / Num. obs: 26504 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rsym value: 0.042 / Net I/σ(I): 37.8 |
Reflection shell | Resolution: 1.73→1.76 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4mi7 Resolution: 1.73→57.1 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.137 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.103
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.084 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→57.1 Å
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Refine LS restraints |
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