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- PDB-5nxu: Complex structure with maltose of Providencia stuartii Omp-Pst1 porin -

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Basic information

Entry
Database: PDB / ID: 5nxu
TitleComplex structure with maltose of Providencia stuartii Omp-Pst1 porin
ComponentsPorin 1
KeywordsCELL 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
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
alpha-maltose / Porin 1
Similarity search - Component
Biological speciesProvidencia stuartii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
B: Porin 1
C: Porin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,52926
Polymers117,1043
Non-polymers5,42623
Water9,674537
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, light scattering, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20400 Å2
ΔGint6 kcal/mol
Surface area42580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.200, 127.120, 150.720
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
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 1 - 352 / Label seq-ID: 1 - 352

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

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: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 3→3.08 Å / Redundancy: 5.34 % / Rmerge(I) obs: 1.34 / Num. unique obs: 2985 / CC1/2: 0.545 / % possible all: 100

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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: 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
RfactorNum. reflection% reflectionSelection details
Rfree0.25489 2030 5 %RANDOM
Rwork0.21095 ---
obs0.21314 38580 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.91 Å20 Å20 Å2
2--3.07 Å20 Å2
3---1.84 Å2
Refinement stepCycle: 1 / Resolution: 3→97.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8274 0 344 537 9155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.028801
X-RAY DIFFRACTIONr_bond_other_d0.0020.028174
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.96511843
X-RAY DIFFRACTIONr_angle_other_deg0.8533.00918054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48151059
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92925.142457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39151359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9621536
X-RAY DIFFRACTIONr_chiral_restr0.170.21206
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210164
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022162
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_it1.546.1534236
X-RAY DIFFRACTIONr_mcbond_other1.546.1524235
X-RAY DIFFRACTIONr_mcangle_it2.6889.2275295
X-RAY DIFFRACTIONr_mcangle_other2.6889.2295296
X-RAY DIFFRACTIONr_scbond_it1.8166.6554565
X-RAY DIFFRACTIONr_scbond_other1.8146.6554565
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1049.8636549
X-RAY DIFFRACTIONr_long_range_B_refined7.58771.7319665
X-RAY DIFFRACTIONr_long_range_B_other7.3871.0889549
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 / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A222200.08
12B222200.08
21A222380.07
22C222380.07
31B226520.07
32C226520.07
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 149 -
Rwork0.348 2832 -
obs--99.93 %
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)
11.603-0.18840.61363.0093-0.16413.12370.00640.04180.30530.0569-0.1618-0.7078-0.35190.34170.15540.2841-0.0569-0.03310.0580.07870.2972-25.914840.7421-36.6389
21.48330.6606-0.35763.4761-0.29572.77450.08080.1662-0.1543-0.5394-0.2682-0.52990.36730.26980.18730.39840.10470.20260.08790.04390.1395-29.7574.9443-48.014
31.1466-0.42120.3714.05060.39512.8767-0.0105-0.34210.01130.7033-0.1115-0.08250.0989-0.06020.1220.46670.0013-0.02450.18540.05010.0425-31.670613.2663-11.1989
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 999
2X-RAY DIFFRACTION2B1 - 999
3X-RAY DIFFRACTION3C1 - 999

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