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Yorodumi- PDB-6qvp: Crystal structure of the peptidoglycan-binding domain of SiiA fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qvp | ||||||
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Title | Crystal structure of the peptidoglycan-binding domain of SiiA from Salmonella enterica | ||||||
Components | Inner membrane protein | ||||||
Keywords | MEMBRANE PROTEIN / OmpA-like domain / Peptidoglycan binding / periplasmic / Salmonella / T1SS | ||||||
Function / homology | membrane => GO:0016020 / PHOSPHATE ION / Inner membrane protein Function and homology information | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Kirchweger, P. / Muller, Y.A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Mol.Microbiol. / Year: 2019 Title: Structural and functional characterization of SiiA, an auxiliary protein from the SPI4-encoded type 1 secretion system from Salmonella enterica. Authors: Kirchweger, P. / Weiler, S. / Egerer-Sieber, C. / Blasl, A.T. / Hoffmann, S. / Schmidt, C. / Sander, N. / Merker, D. / Gerlach, R.G. / Hensel, M. / Muller, Y.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qvp.cif.gz | 371.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qvp.ent.gz | 326.3 KB | Display | PDB format |
PDBx/mmJSON format | 6qvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/6qvp ftp://data.pdbj.org/pub/pdb/validation_reports/qv/6qvp | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 11926.239 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: siiA, DD95_13055, EIL76_22260 / Production host: Escherichia coli (E. coli) / References: UniProt: H9L4G5 #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: 2.77 Å3/Da / Density % sol: 55.64 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9.1 Details: 0.2 M Sodium phosphate dibasic dihydrate, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 29, 2014 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→42.5 Å / Num. obs: 57795 / % possible obs: 95.9 % / Redundancy: 1.7 % / Biso Wilson estimate: 17.81 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.114 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.9→2.01 Å / Mean I/σ(I) obs: 2.3 / CC1/2: 0.72 / Rrim(I) all: 0.54 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→19.964 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.964 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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