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- PDB-6zre: Deciphering the role of the channel constrictions in the opening ... -

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Basic information

Entry
Database: PDB / ID: 6zre
TitleDeciphering the role of the channel constrictions in the opening mechanism of MexAB-OprM efflux pump from Pseudomonas aeruginosa
ComponentsOuter membrane protein OprM
KeywordsTRANSLOCASE / Efflux pump / antibiotic resistance / TolC-like / outer-membrane channel.
Function / homology
Function and homology information


efflux transmembrane transporter activity / transmembrane transporter activity / cell outer membrane / transmembrane transport / response to antibiotic / membrane
Similarity search - Function
RND efflux system, outer membrane lipoprotein, NodT / Outer membrane efflux protein / Outer membrane efflux protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
PALMITIC ACID / Outer membrane protein OprM
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNtsogo Enguene, Y.V. / Monlezun, L. / Ma, M. / Garnier, C. / Lascombe, M.B. / Salem, M. / Guenard, S. / Plesiat, P. / Llanes, C. / Phan, G. / Broutin, I.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BSV8-0010-01 France
CitationJournal: To Be Published
Title: Deciphering the role of OprM constrictions in the opening mechanism of the MexAB-OprM efflux pump from Pseudomonas aeruginosa.
Authors: Ntsogo Enguene, Y.V. / Monlezun, L. / Ma, M. / Garnier, C. / Lascombe, M.B. / Salem, M. / Guenard, S. / Plesiat, P. / Llanes, C. / Phan, G. / Broutin, I.
History
DepositionJul 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 2.0Jul 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / database_2 / entity / entity_src_gen / pdbx_audit_support / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_shell / reflns / reflns_shell / software / struct_asym / struct_conf / struct_conn / struct_keywords / struct_sheet_range
Item: _citation.title / _database_2.pdbx_DOI ..._citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant / _pdbx_audit_support.grant_number / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_R_Free_selection_details / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_high / _reflns.d_resolution_low / _reflns.number_obs / _reflns.pdbx_CC_half / _reflns.pdbx_CC_star / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_redundancy / _reflns.percent_possible_obs / _software.version / _struct_keywords.text / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id
Description: Real space R-factor / Provider: author / Type: Coordinate replacement
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein OprM
B: Outer membrane protein OprM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,66315
Polymers103,0952
Non-polymers3,56913
Water00
1
A: Outer membrane protein OprM
hetero molecules

A: Outer membrane protein OprM
hetero molecules

A: Outer membrane protein OprM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,34842
Polymers154,6423
Non-polymers10,70639
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area21840 Å2
ΔGint-95 kcal/mol
Surface area61220 Å2
MethodPISA
2
B: Outer membrane protein OprM

B: Outer membrane protein OprM

B: Outer membrane protein OprM


Theoretical massNumber of molelcules
Total (without water)154,6423
Polymers154,6423
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area15090 Å2
ΔGint-95 kcal/mol
Surface area60880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.797, 86.797, 1046.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Outer membrane protein OprM


Mass: 51547.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Acylation of the N-terminal cyteine
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: oprM, oprK, PA0427 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q51487
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#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.: 11
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Has ligand of interestY

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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: 3.68 Å3/Da / Density % sol: 66.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: sodium sulfate, lithium sulfate, PEG 400, Tris-HCl

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.8→47.63 Å / Num. obs: 38761 / % possible obs: 99.48 % / Redundancy: 2 % / Biso Wilson estimate: 93.04 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.0167 / Rrim(I) all: 0.02361 / Net I/σ(I): 15.77
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.92101.4894592145880.8880.4951.5711.599.7
9.7-49.348.10.034871710760.9980.0130.03645.798.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D5K

3d5k


Resolution: 2.8→47.63 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 40.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3175 1888 5 %Random selection
Rwork0.2928 36742 --
obs-38629 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.01 Å2 / Biso mean: 119.95 Å2 / Biso min: 53.62 Å2
Refinement stepCycle: final / Resolution: 2.8→47.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6964 0 240 0 7204
Biso mean--115.32 --
Num. residues----910
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.880.47671300.42252730286099
2.88-2.960.47011290.42882757288699
2.96-3.060.48481450.47682755290099
3.06-3.170.45911440.397727802924100
3.17-3.290.36441530.338727832936100
3.29-3.440.34811380.312627992937100
3.44-3.620.35931240.331728402964100
3.62-3.850.29951530.292627862939100
3.85-4.150.30411750.265828192994100
4.15-4.560.28811290.250228672996100
4.56-5.220.2621560.247528352991100
5.22-6.580.28081400.28629273067100
6.58-49.340.32561720.28983064323699

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