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Yorodumi- PDB-5nxu: Complex structure with maltose of Providencia stuartii Omp-Pst1 porin -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nxu | ||||||||||||
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Title | Complex structure with maltose of Providencia stuartii Omp-Pst1 porin | ||||||||||||
Components | Porin 1 | ||||||||||||
Keywords | CELL ADHESION / 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 Å | ||||||||||||
Authors | Colletier, J.P. / Nasrallah, C. | ||||||||||||
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 | 5nxu.cif.gz | 449.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nxu.ent.gz | 377.6 KB | Display | PDB format |
PDBx/mmJSON format | 5nxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nxu_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5nxu_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5nxu_validation.xml.gz | 47.5 KB | Display | |
Data in CIF | 5nxu_validation.cif.gz | 66.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/5nxu ftp://data.pdbj.org/pub/pdb/validation_reports/nx/5nxu | HTTPS FTP |
-Related structure data
Related structure data | 4d64SC 4d65C 5n9hC 5n9iC 5nxnC 5nxrC 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: _ / 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 - 352
NCS ensembles :
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-Components
#1: Protein | Mass: 39034.527 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: Polysaccharide | #3: Chemical | ChemComp-LDA / #4: Chemical | ChemComp-CA / | #5: 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: 4.8 Å3/Da / Density % sol: 74.4 % / Description: Rods |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 14% PEG 6000 MME, 0.1 M MES pH 6.5, 0.1 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2010 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3→97.7 Å / Num. obs: 40456 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 5.04 % / Biso Wilson estimate: 81.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.114 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 3→3.08 Å / Redundancy: 5.34 % / Rmerge(I) obs: 1.34 / Num. unique obs: 2985 / CC1/2: 0.545 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4D64 Resolution: 3→97.17 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.903 / SU B: 32.864 / SU ML: 0.318 / Cross valid method: THROUGHOUT / ESU R: 1.434 / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 97.9 Å2
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Refinement step | Cycle: 1 / Resolution: 3→97.17 Å
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Refine LS restraints |
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