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- PDB-5n9i: STRUCTURE OF 206-GVVTSE-211, THE STERIC ZIPPER THAT SUPPORTS THE ... -

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Basic information

Entry
Database: PDB / ID: 5n9i
TitleSTRUCTURE OF 206-GVVTSE-211, THE STERIC ZIPPER THAT SUPPORTS THE SELF-ASSOCIATION OF P. STUARTII OMP-PST1 INTO DIMERS OF TRIMERS
ComponentsPorin 1
KeywordsCELL 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
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / Porin domain superfamily
Similarity search - Domain/homology
Biological speciesProvidencia stuartii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsColletier, J.P. / Nasrallah, C.
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 1
B: Porin 1
C: Porin 1
D: Porin 1


Theoretical massNumber of molelcules
Total (without water)2,3624
Polymers2,3624
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-2 kcal/mol
Surface area2930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)4.800, 16.910, 45.450
Angle α, β, γ (deg.)90.05, 90.01, 90.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
Porin 1 /


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 / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 1.62 Å3/Da / Density % sol: 23.9 % / Description: Needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 2.5 M AMONIUM SULFATE, 0.1 M ACID CITRIC PH4 / PH range: 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9731
20.8731
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.298
11-h,-k,l20.198
11h,-k,-l30.288
11-H, K, -L40.216
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 168 15.9 %RANDOM
Rwork0.14735 ---
obs0.15705 890 92.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.675 Å2
Baniso -1Baniso -2Baniso -3
1--7.24 Å215.14 Å2-15.62 Å2
2--24.21 Å2-0.38 Å2
3----16.97 Å2
Refinement stepCycle: 1 / Resolution: 1.91→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms164 0 0 18 182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02160
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2292.026216
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.322520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg56.565304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1741524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1380.232
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.906→1.956 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.532 10 -
Rwork0.208 88 -
obs--96.08 %

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