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- PDB-5nxr: Trimeric structure of Omp-Pst1, the major porin from Providencia ... -

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Basic information

Entry
Database: PDB / ID: 5nxr
TitleTrimeric structure of Omp-Pst1, the major porin from Providencia stuartii
ComponentsPorin 1
KeywordsCELL ADHESION / porins / cell-to-cell contact / adhesive junctions / biofilms / steric zipper
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
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 / : / Porin domain superfamily / Porin ...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 / : / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesProvidencia stuartii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsColletier, J.P. / Nasrallah, C.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research AgencyANR-10-INSB-05-02 France
French National Research AgencyANR-10-LABX-49-01 France
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
DepositionMay 10, 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
Revision 2.0Feb 6, 2019Group: Advisory / Atomic model / Data collection / Category: atom_site / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id
Revision 2.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Porin 1
C: Porin 1
B: Porin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,69677
Polymers117,1043
Non-polymers16,59274
Water15,025834
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, native gel electrophoresis, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38770 Å2
ΔGint201 kcal/mol
Surface area48190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.840, 129.000, 159.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22B
13C
23B

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA1 - 3501 - 350
21TYRTYRCB1 - 3501 - 350
12TYRTYRAA1 - 3501 - 350
22TYRTYRBC1 - 3501 - 350
13PHEPHECB1 - 3521 - 352
23PHEPHEBC1 - 3521 - 352

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Porin 1


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: Chemical...
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 72 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 834 / 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: 4.8 Å3/Da / Density % sol: 74.4 % / Description: rods
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.7→87.03 Å / Num. obs: 57401 / % possible obs: 90.6 % / Observed criterion σ(I): 2 / Redundancy: 4.36 % / Biso Wilson estimate: 59.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Net I/σ(I): 23.48
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 4.14 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 3376 / CC1/2: 0.824 / % possible all: 73.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D64

4d64


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.898 / SU B: 29.424 / SU ML: 0.318 / Cross valid method: THROUGHOUT / ESU R: 0.549 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28537 2960 5 %RANDOM
Rwork0.23716 ---
obs0.23958 56251 94.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.531 Å2
Baniso -1Baniso -2Baniso -3
1--6.23 Å20 Å20 Å2
2--1 Å20 Å2
3---5.23 Å2
Refinement stepCycle: 1 / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8274 0 1037 834 10145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.029578
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3712.02312715
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68451070
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90625.184463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.739151367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6551536
X-RAY DIFFRACTIONr_chiral_restr0.2130.21234
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026798
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_it1.0162.2564265
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8293.3795340
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3364.0275313
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.37952.04338442
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A22292
12C22292
21A22308
22B22308
31C22574
32B22574
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 211 -
Rwork0.437 4019 -
obs--94.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2697-0.18160.55552.08450.39412.3313-0.02890.14310.3705-0.049-0.0004-0.3784-0.21580.33270.02930.8004-0.0518-0.01630.32090.08290.338-27.79839.587-40.012
21.91680.1935-0.23842.1838-0.26822.22310.15730.2461-0.1307-0.0505-0.0437-0.03720.21060.243-0.11360.83610.0829-0.02940.3566-0.09310.0476-33.623.969-51.93
31.6172-0.5020.57362.9859-0.14412.4576-0.0047-0.3109-0.07570.17280.03170.00390.0502-0.0138-0.02710.78790.0448-0.01970.40180.02160.0043-33.1411.687-14.771
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 352
2X-RAY DIFFRACTION2C1 - 352
3X-RAY DIFFRACTION3B1 - 352

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