+Open data
-Basic information
Entry | Database: PDB / ID: 4yx1 | ||||||
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Title | SpaO(SPOA2) | ||||||
Components | Surface presentation of antigens protein SpaO | ||||||
Keywords | PROTEIN TRANSPORT / Type III Secretion System | ||||||
Function / homology | Function and homology information bacterial-type flagellum-dependent swarming motility / protein secretion by the type III secretion system / positive chemotaxis Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å | ||||||
Authors | Notti, R.Q. / Stebbins, C.E. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: A common assembly module in injectisome and flagellar type III secretion sorting platforms. Authors: Notti, R.Q. / Bhattacharya, S. / Lilic, 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 | 4yx1.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yx1.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 4yx1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/4yx1 ftp://data.pdbj.org/pub/pdb/validation_reports/yx/4yx1 | 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
#1: Protein | Mass: 7851.493 Da / Num. of mol.: 2 / Fragment: UNP Residues 232-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: spaO, STM2891 / Production host: Escherichia coli (E. coli) / References: UniProt: P40699 #2: Chemical | #3: 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: 2.14 Å3/Da / Density % sol: 42.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: SpaO(232-297) was concentrated to 8mg/mL and crystallized with 35% PEG400, 200mM calcium acetate, 100mM sodium acetate pH=5.0. Crystals were cryoprotected in the mother liquor. Microseeding ...Details: SpaO(232-297) was concentrated to 8mg/mL and crystallized with 35% PEG400, 200mM calcium acetate, 100mM sodium acetate pH=5.0. Crystals were cryoprotected in the mother liquor. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.35→41.27 Å / Num. obs: 29266 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.059 / Net I/σ(I): 8.6 / Num. measured all: 203967 / Scaling rejects: 17 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.35→31.262 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.17 / Stereochemistry target values: ML
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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 max: 54.09 Å2 / Biso mean: 17.7123 Å2 / Biso min: 5.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→31.262 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28
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