+Open data
-Basic information
Entry | Database: PDB / ID: 2fm9 | ||||||
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Title | Structure of Salmonella SipA residues 48-264 | ||||||
Components | Cell invasion protein sipA | ||||||
Keywords | CELL INVASION / Salmonella / type II secretion / SipA / virulence / bacterial | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Lilic, M. / Vujanac, M. / Stebbins, C.E. | ||||||
Citation | Journal: Mol.Cell / Year: 2006 Title: A common structural motif in the binding of virulence factors to bacterial secretion chaperones. Authors: Lilic, M. / Vujanac, M. / Stebbins, C.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fm9.cif.gz | 52.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fm9.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 2fm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/2fm9 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/2fm9 | HTTPS FTP |
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-Related structure data
-Links
-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: 23582.234 Da / Num. of mol.: 1 / Fragment: Residues 48-264 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: sipA, sspA / Plasmid: pGEX-4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q56027, UniProt: P0CL52*PLUS |
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#2: 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: 2.95 Å3/Da / Density % sol: 58.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: hanging drops formed from mixing a 1:1 volume ratio of 20mg/ml protein with an equilibration buffer consisting of 20% PEG6000, 20% glycerol, Na-citrate pH 5.6 and 0.01M adenosine-5 - ...Details: hanging drops formed from mixing a 1:1 volume ratio of 20mg/ml protein with an equilibration buffer consisting of 20% PEG6000, 20% glycerol, Na-citrate pH 5.6 and 0.01M adenosine-5 -triphosphate disodium salt (ATP) as an additive., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→99 Å / Num. all: 19209 / Num. obs: 19209 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.031 / Χ2: 1.018 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.357 / Num. unique all: 1888 / Χ2: 1.064 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.455 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.37 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 15.339 Å / Origin y: 43.483 Å / Origin z: 17.002 Å
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Refinement TLS group | Selection: ALL |