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- PDB-5n9h: STRUCTURE OF 283-LGNY-286, THE STERIC ZIPPER THAT SUPPORTS THE SE... -

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Basic information

Entry
Database: PDB / ID: 5n9h
TitleSTRUCTURE OF 283-LGNY-286, THE STERIC ZIPPER THAT SUPPORTS THE SELF-ASSOCIATION OF P. STUARTII OMP-PST2 INTO DIMERS OF TRIMERS
ComponentsPorin
KeywordsCELL ADHESION / STERIC-ZIPPER / PORIN / MICRO-CRYSTAL / SELF-ASSOCIATION
Function / homology:
Function and homology information
Biological speciesProvidencia stuartii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.997 Å
AuthorsNasrallah, C. / Colletier, J.P.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE18-0005-02 France
CitationJournal: 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
DepositionFeb 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Porin
B: Porin
C: Porin
M: Porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,0546
Polymers1,8624
Non-polymers1922
Water1448
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-15 kcal/mol
Surface area2700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)4.784, 11.546, 47.044
Angle α, β, γ (deg.)90.01, 90.01, 90.01
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
Porin /


Mass: 465.501 Da / Num. of mol.: 4 / Fragment: DIMERIZATION DOMAIN, UNP residues 305-308 / Source method: obtained synthetically / Source: (synth.) Providencia stuartii (bacteria) / References: UniProt: A0A0L6X8Y0
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.45 Å3/Da / Density % sol: 15.4 % / Description: Needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 3.2 M AMMONIUM SULFATE; 0.1 M BUFFER ACID CITRIC PH4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 0.997→47.04 Å / Num. obs: 4934 / % possible obs: 89.7 % / Observed criterion σ(I): 5.5 / Redundancy: 2.17 % / Biso Wilson estimate: 1.68 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.81
Reflection shellResolution: 1→1.06 Å / Redundancy: 2.12 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5.47 / % possible all: 87.4

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
SHELXEphasing
PHENIXrefinement
SHELXLphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.997→23.522 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 2.03 / Phase error: 8.97
RfactorNum. reflection% reflection
Rfree0.0959 246 5 %
Rwork0.0811 --
obs0.0818 4918 89.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 0 Å2 / ksol: 0 e/Å3
Displacement parametersBiso mean: 2.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.1048 Å20.3781 Å2-0.0048 Å2
2---0.422 Å20.3629 Å2
3----0.2565 Å2
Refinement stepCycle: LAST / Resolution: 0.997→23.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms132 0 10 8 150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013148
X-RAY DIFFRACTIONf_angle_d1.929200
X-RAY DIFFRACTIONf_dihedral_angle_d11.33844
X-RAY DIFFRACTIONf_chiral_restr0.11316
X-RAY DIFFRACTIONf_plane_restr0.00724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9972-1.25640.11671210.09712306X-RAY DIFFRACTION87
1.2564-23.52850.08311250.07162366X-RAY DIFFRACTION91

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