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Yorodumi- PDB-5nxn: Structure of a L5-deletion mutant of Providencia stuartii Omp-Pst1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nxn | ||||||||||||
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Title | Structure of a L5-deletion mutant of Providencia stuartii Omp-Pst1 | ||||||||||||
Components | Porin 1 | ||||||||||||
Keywords | TRANSPORT PROTEIN / porins / cell-to-cell contact / adhesive junctions / biofilms / steric zipper | ||||||||||||
Function / homology | Function and homology information porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane Similarity search - Function | ||||||||||||
Biological species | Providencia stuartii (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å | ||||||||||||
Authors | El Khatib, M. / Colletier, J.P. | ||||||||||||
Funding support | France, 3items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nxn.cif.gz | 429 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nxn.ent.gz | 358.8 KB | Display | PDB format |
PDBx/mmJSON format | 5nxn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/5nxn ftp://data.pdbj.org/pub/pdb/validation_reports/nx/5nxn | 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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / 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.) Providencia stuartii (bacteria) / Plasmid: pGOmpF Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: E3U904 #2: Chemical | ChemComp-CA / | #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: 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: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.93 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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