+Open data
-Basic information
Entry | Database: PDB / ID: 5lp9 | ||||||
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Title | FimA wt from S. flexneri | ||||||
Components | Major type 1 subunit fimbrin (Pilin) | ||||||
Keywords | STRUCTURAL PROTEIN / FimA / pilus / monomer / subunit / pili / Shigella / flexneri / pathogenic / main structural subunit / high resolution | ||||||
Function / homology | Fimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / pilus / cell adhesion / Major type 1 subunit fimbrin (Pilin) / Major type 1 subunit fimbrin (Pilin) Function and homology information | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.886266337349 Å | ||||||
Authors | Zyla, D. / Capitani, G. / Prota, A. / Glockshuber, R. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Alternative folding to a monomer or homopolymer is a common feature of the type 1 pilus subunit FimA from enteroinvasive bacteria. Authors: Zyla, D.S. / Prota, A.E. / Capitani, G. / Glockshuber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lp9.cif.gz | 142.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lp9.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 5lp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/5lp9 ftp://data.pdbj.org/pub/pdb/validation_reports/lp/5lp9 | HTTPS FTP |
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-Related structure data
Related structure data | 5nktC 6erjC 2m5gS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/m35lp9 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16416.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: fimA, S4465, SF4208, AJR25_020510, AJR27_013385 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q83P68, UniProt: A0A0H2V3I0*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: 1.75 Å3/Da / Density % sol: 29.8 % / Description: 3-dimensional crystal, with irregular shape |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3 Details: 0.1M Sodium Malonate, pH 3.0, 40% ammonium sulphate saturated at 277 K, 23 mg/ml of protein, 1:1 mixture PH range: 2.0-3.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 15, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 0.85→26.89 Å / Num. obs: 89042 / % possible obs: 80.3 % / Observed criterion σ(I): -3 / Redundancy: 5.423 % / Biso Wilson estimate: 8.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.042 / Χ2: 0.998 / Net I/σ(I): 20.03 / Num. measured all: 482856 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2M5G model 1 Resolution: 0.886266337349→26.89 Å / SU ML: 0.0498525365341 / Cross valid method: FREE R-VALUE / σ(F): 1.38946530496 / Phase error: 13.0544129219 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 19.6351376835 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.886266337349→26.89 Å
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Refine LS restraints |
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LS refinement shell |
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