+Open data
-Basic information
Entry | Database: PDB / ID: 4yx5 | ||||||
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Title | SpaO(SPOA1,2) | ||||||
Components | (Surface presentation of antigens protein SpaO) x 2 | ||||||
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: 2.9001 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 | 4yx5.cif.gz | 40.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yx5.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 4yx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yx5_validation.pdf.gz | 428.5 KB | Display | wwPDB validaton report |
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Full document | 4yx5_full_validation.pdf.gz | 430.6 KB | Display | |
Data in XML | 4yx5_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 4yx5_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/4yx5 ftp://data.pdbj.org/pub/pdb/validation_reports/yx/4yx5 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 8246.572 Da / Num. of mol.: 1 / Fragment: UNP Residues 145-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: spaO, STM2891 / Production host: Escherichia coli (E. coli) / References: UniProt: P40699 |
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#2: Protein | Mass: 7710.809 Da / Num. of mol.: 1 / 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 |
#3: Chemical | ChemComp-CL / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: SpaO(145-213) + SpaO (232-297) was concentrated to 12mg/mL and crystallized with 25% PEG400, 10% isopropanol, 100mM sodium citrate pH=5.6 at 277K. Microseeding was employed to enhance ...Details: SpaO(145-213) + SpaO (232-297) was concentrated to 12mg/mL and crystallized with 25% PEG400, 10% isopropanol, 100mM sodium citrate pH=5.6 at 277K. 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. Crystals were cryoprotected in mother liquor with the PEG400 concentration raised to 37.5%. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075, 0.979 | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.9→54.19 Å / Num. obs: 4975 / % possible obs: 99.3 % / Redundancy: 24.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.034 / Net I/σ(I): 14.4 / Num. measured all: 122494 / Scaling rejects: 9 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.9001→38.678 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.3 / 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: 154.08 Å2 / Biso mean: 74.2199 Å2 / Biso min: 37.22 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9001→38.678 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: 4 / % reflection obs: 99 %
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