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- PDB-5nxn: Structure of a L5-deletion mutant of Providencia stuartii Omp-Pst1 -

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Basic information

Entry
Database: PDB / ID: 5nxn
TitleStructure of a L5-deletion mutant of Providencia stuartii Omp-Pst1
ComponentsPorin 1
KeywordsTRANSPORT PROTEIN / 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. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin ...Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / 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: 3.12 Å
AuthorsEl Khatib, M. / Colletier, J.P.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE18-0005-02 France
French National Research AgencyANR-10-LABX-49-01 France
French National Research AgencyANR-10-INSB-05-02 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 1.3Jan 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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)113,6694
Polymers113,6293
Non-polymers401
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10150 Å2
ΔGint-52 kcal/mol
Surface area41430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.321, 158.985, 101.326
Angle α, β, γ (deg.)90.00, 124.65, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 1 - 352 / Label seq-ID: 1 - 342

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: 37876.359 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-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 520 / 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: 3.7 Å3/Da / Density % sol: 66.7 % / Description: Rod-like crystals
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 600, 0.2 M NaCl, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.93 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2016 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 3.11→50 Å / Num. obs: 29184 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 6.78 % / Biso Wilson estimate: 70.279 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.202 / Net I/σ(I): 8.16
Reflection shellResolution: 3.11→3.21 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.681 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 2342 / CC1/2: 0.605 / % possible all: 79.2

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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: 3.12→50 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.911 / SU B: 58.154 / SU ML: 0.5 / Cross valid method: THROUGHOUT / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26795 1481 5.1 %RANDOM
Rwork0.2462 ---
obs0.24735 27554 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.919 Å2
Baniso -1Baniso -2Baniso -3
1-3.28 Å20 Å21.5 Å2
2--0.02 Å20 Å2
3----2.75 Å2
Refinement stepCycle: 1 / Resolution: 3.12→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8028 0 1 520 8549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.028308
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.93211222
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.04151044
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11925.135446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.613151348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3141536
X-RAY DIFFRACTIONr_chiral_restr0.1490.21128
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.026600
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_it1.6063.8144158
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8375.7145208
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4553.8574147
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.24776.92137908
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 / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A194980.21
12B194980.21
21A195620.22
22C195620.22
31B195280.21
32C195280.21
LS refinement shellResolution: 3.116→3.197 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 95 -
Rwork0.405 1773 -
obs--85.18 %
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)
13.40040.6120.36641.96530.23252.84720.09090.33850.1521-0.239-0.01390.234-0.1313-0.4992-0.0771.15370.12580.18640.17170.14840.458629.398412.88418.095
21.6039-0.38740.51421.78430.14512.6734-0.0075-0.16350.11550.0979-0.0018-0.14150.08060.36810.00931.0283-0.02680.2380.0935-0.00580.412857.2887-0.452630.5313
32.3004-0.0610.6941.66440.24013.0753-0.14260.1003-0.3884-0.00580.02180.30580.4392-0.41690.12081.1223-0.07660.24430.0794-0.07040.465134.0809-24.760612.3864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 352
2X-RAY DIFFRACTION2B1 - 352
3X-RAY DIFFRACTION3C1 - 352

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