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Yorodumi- PDB-5n9i: STRUCTURE OF 206-GVVTSE-211, THE STERIC ZIPPER THAT SUPPORTS THE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n9i | ||||||
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Title | STRUCTURE OF 206-GVVTSE-211, THE STERIC ZIPPER THAT SUPPORTS THE SELF-ASSOCIATION OF P. STUARTII OMP-PST1 INTO DIMERS OF TRIMERS | ||||||
Components | Porin 1 | ||||||
Keywords | CELL ADHESION / STERIC-ZIPPER / PORIN / MICRO-CRYSTAL / SELF-ASSOCIATION | ||||||
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: 1.91 Å | ||||||
Authors | Colletier, J.P. / Nasrallah, C. | ||||||
Funding support | France, 1items
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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 | 5n9i.cif.gz | 12.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n9i.ent.gz | 7.9 KB | Display | PDB format |
PDBx/mmJSON format | 5n9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n9i_validation.pdf.gz | 426.7 KB | Display | wwPDB validaton report |
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Full document | 5n9i_full_validation.pdf.gz | 426.6 KB | Display | |
Data in XML | 5n9i_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 5n9i_validation.cif.gz | 3.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/5n9i ftp://data.pdbj.org/pub/pdb/validation_reports/n9/5n9i | HTTPS FTP |
-Related structure data
Related structure data | 4d64C 4d65C 5n9hC 5nxnC 5nxrC 5nxuC 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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-Components
#1: Protein/peptide | Mass: 590.624 Da / Num. of mol.: 4 / Fragment: DIMERIZATION DOMAIN, UNP residues 228-233 / Source method: obtained synthetically / Source: (synth.) Providencia stuartii (bacteria) / References: UniProt: E3U904 #2: 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: 1.62 Å3/Da / Density % sol: 23.9 % / Description: Needles |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 2.5 M AMONIUM SULFATE, 0.1 M ACID CITRIC PH4 / PH range: 4 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å | |||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 18, 2012 | |||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.91→50 Å / Num. obs: 1076 / % possible obs: 96.66 % / Observed criterion σ(I): 3 / Redundancy: 2.2 % / Biso Wilson estimate: 15.748 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.1197 / Rpim(I) all: 0.1088 / Rrim(I) all: 0.1623 / Net I/σ(I): 4.9 | |||||||||||||||||||||||||
Reflection shell | Resolution: 1.91→1.979 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.1879 / Mean I/σ(I) obs: 3.24 / Num. unique obs: 122 / CC1/2: 0.973 / Rpim(I) all: 0.169 / Rrim(I) all: 0.2535 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: a canonical beta-sheet Resolution: 1.91→45.45 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.112 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 12.675 Å2
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Refinement step | Cycle: 1 / Resolution: 1.91→45.45 Å
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Refine LS restraints |
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