+Open data
-Basic information
Entry | Database: PDB / ID: 6ai1 | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the 328-692 fragment of FlhA (D456V) | |||||||||||||||||||||
Components | Flagellar biosynthesis protein FlhA | |||||||||||||||||||||
Keywords | PROTEIN TRANSPORT / flagellar type III secretion | |||||||||||||||||||||
Function / homology | Function and homology information | |||||||||||||||||||||
Biological species | Salmonella typhimurium (bacteria) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å | |||||||||||||||||||||
Authors | Ogawa, Y. / Kinoshita, M. / Minamino, T. / Imada, K. | |||||||||||||||||||||
Funding support | Japan, 6items
| |||||||||||||||||||||
Citation | Journal: Structure / Year: 2019 Title: Structural Insights into the Substrate Specificity Switch Mechanism of the Type III Protein Export Apparatus. Authors: Inoue, Y. / Ogawa, Y. / Kinoshita, M. / Terahara, N. / Shimada, M. / Kodera, N. / Ando, T. / Namba, K. / Kitao, A. / Imada, K. / Minamino, T. | |||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ai1.cif.gz | 144.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ai1.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ai1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ai1_validation.pdf.gz | 443 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ai1_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | 6ai1_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 6ai1_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/6ai1 ftp://data.pdbj.org/pub/pdb/validation_reports/ai/6ai1 | HTTPS FTP |
-Related structure data
Related structure data | 6ai0C 6ai2C 6ai3C 3a5iS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40655.688 Da / Num. of mol.: 2 / Fragment: cytoplasmic fragment, residues 328-692 / Mutation: D456V 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: flhA, STM1913 / Plasmid: pGEX6p1 Production host: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain (production host): SJW1368 / References: UniProt: P40729 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.69 Å3/Da / Density % sol: 73.8 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG-400, 0.1M HEPES pH 7.5, 0.25M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→68.6 Å / Num. obs: 19380 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 68.3 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 3.5→3.83 Å / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4609 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A5I Resolution: 3.5→54.198 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.37
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 190.04 Å2 / Biso mean: 94.8251 Å2 / Biso min: 39.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→54.198 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
|