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- PDB-5nxn: Structure of a L5-deletion mutant of Providencia stuartii Omp-Pst1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nxn | ||||||||||||
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Title | Structure of a L5-deletion mutant of Providencia stuartii Omp-Pst1 | ||||||||||||
![]() | Porin 1 | ||||||||||||
![]() | TRANSPORT PROTEIN / porins / cell-to-cell contact / adhesive junctions / biofilms / steric zipper | ||||||||||||
Function / homology | ![]() porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | El Khatib, M. / Colletier, J.P. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Porin self-association enables cell-to-cell contact in Authors: El-Khatib, M. / Nasrallah, C. / Lopes, J. / Tran, Q.T. / Tetreau, G. / Basbous, H. / Fenel, D. / Gallet, B. / Lethier, M. / Bolla, J.M. / Pages, J.M. / Vivaudou, M. / Weik, M. / ...Authors: El-Khatib, M. / Nasrallah, C. / Lopes, J. / Tran, Q.T. / Tetreau, G. / Basbous, H. / Fenel, D. / Gallet, B. / Lethier, M. / Bolla, J.M. / Pages, J.M. / Vivaudou, M. / Weik, M. / Winterhalter, M. / Colletier, J.P. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 429 KB | Display | ![]() |
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PDB format | ![]() | 358.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4d64SC ![]() 4d65C ![]() 5n9hC ![]() 5n9iC ![]() 5nxrC ![]() 5nxuC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 1 - 352 / Label seq-ID: 1 - 342
NCS ensembles :
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Components
#1: Protein | Mass: 37876.359 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: E3U904 #2: Chemical | ChemComp-CA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.7 % / Description: Rod-like crystals |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 600, 0.2 M NaCl, 0.1 M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2016 / Details: Toroidal mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 3.11→50 Å / Num. obs: 29184 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 6.78 % / Biso Wilson estimate: 70.279 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.202 / Net I/σ(I): 8.16 |
Reflection shell | Resolution: 3.11→3.21 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.681 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 2342 / CC1/2: 0.605 / % possible all: 79.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4D64 Resolution: 3.12→50 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.911 / SU B: 58.154 / SU ML: 0.5 / Cross valid method: THROUGHOUT / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.919 Å2
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Refinement step | Cycle: 1 / Resolution: 3.12→50 Å
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Refine LS restraints |
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