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- PDB-5iuy: Structural insights of the outer-membrane channel OprN -

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Basic information

Entry
Database: PDB / ID: 5iuy
TitleStructural insights of the outer-membrane channel OprN
ComponentsMultidrug efflux outer membrane protein OprN
KeywordsTRANSPORT PROTEIN / Efflux pumps / OMF / membrane protein / antibiotics resistance
Function / homology
Function and homology information


efflux transmembrane transporter activity / transmembrane transporter activity / cell outer membrane / transmembrane transport / membrane
Similarity search - Function
Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / RND efflux system, outer membrane lipoprotein, NodT / Outer membrane efflux protein / Outer membrane efflux protein / Single Sheet / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / PALMITIC ACID / Multidrug efflux outer membrane protein OprN
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsNtsogo, Y. / Garnier, C. / Phan, G. / Monlezun, L. / Benas, P. / Broutin, I.
Funding support France, 1items
OrganizationGrant numberCountry
ANR Assembly and Association "Vaincre la MucoviscidoseANR-12-BSV8-0010-01 and RF20130500918 France
CitationJournal: PLoS ONE / Year: 2017
Title: Xenon for tunnelling analysis of the efflux pump component OprN.
Authors: Ntsogo Enguene, Y.V. / Phan, G. / Garnier, C. / Ducruix, A. / Prange, T. / Broutin, I.
History
DepositionMar 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / pdbx_related_exp_data_set / Item: _audit_author.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multidrug efflux outer membrane protein OprN
B: Multidrug efflux outer membrane protein OprN
C: Multidrug efflux outer membrane protein OprN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,89014
Polymers148,6263
Non-polymers2,26411
Water12,268681
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18990 Å2
ΔGint-63 kcal/mol
Surface area58030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)257.648, 257.648, 81.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein Multidrug efflux outer membrane protein OprN


Mass: 49542.059 Da / Num. of mol.: 3 / Fragment: UNP residues 26-472
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: oprN, PA2495 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I0Y7
#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 689 molecules

#2: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C16H32O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / 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: 4.55 Å3/Da / Density % sol: 72.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium acetate pH 5.4, 0.8 M Sodium formate, 11% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.29→182.185 Å / Num. obs: 119764 / % possible obs: 99.4 % / Redundancy: 4.88 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 8.04
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 4.49 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 1.76 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D5K

3d5k


Resolution: 2.29→182.18 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.752 / SU ML: 0.113 / Cross valid method: FREE R-VALUE / ESU R: 0.177 / ESU R Free: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.22536 6012 5 %RANDOM
Rwork0.18805 ---
obs0.18993 113747 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.643 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.29→182.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10316 0 100 681 11097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01910648
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210188
X-RAY DIFFRACTIONr_angle_refined_deg2.0741.97514409
X-RAY DIFFRACTIONr_angle_other_deg1.085323274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91151357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33322.868537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.906151760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8215149
X-RAY DIFFRACTIONr_chiral_restr0.1050.21607
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022519
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_it2.9883.255392
X-RAY DIFFRACTIONr_mcbond_other2.9883.255393
X-RAY DIFFRACTIONr_mcangle_it4.0094.8536740
X-RAY DIFFRACTIONr_mcangle_other4.0094.8546741
X-RAY DIFFRACTIONr_scbond_it4.5923.8645256
X-RAY DIFFRACTIONr_scbond_other4.5923.8645254
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8565.5727663
X-RAY DIFFRACTIONr_long_range_B_refined8.56530.89245281
X-RAY DIFFRACTIONr_long_range_B_other8.56930.87344888
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.349 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 454 -
Rwork0.271 8401 -
obs--99.52 %

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