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- PDB-7akz: Deciphering the role of the channel constrictions in the opening ... -

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Basic information

Entry
Database: PDB / ID: 7akz
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 / 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: 3.2 Å
AuthorsNtsogo Enguene, V.Y. / 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 Agency France
CitationJournal: To Be Published
Title: Deciphering the role of the channel constrictions in the opening mechanism of MexAB-OprM efflux pump from Pseudomonas aeruginosa
Authors: Ntsogo Enguene, V.Y. / Monlezun, L. / Ma, M. / Garnier, C. / Lascombe, M.B. / Salem, M. / Guenard, S. / Plesiat, P. / Llanes, C. / Phan, G. / Broutin, I.
History
DepositionOct 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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

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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)104,1166
Polymers102,9832
Non-polymers1,1344
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)157,87515
Polymers154,4743
Non-polymers3,40112
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 area18890 Å2
ΔGint-66 kcal/mol
Surface area61240 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)154,4743
Polymers154,4743
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area15500 Å2
ΔGint-92 kcal/mol
Surface area60190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.059, 86.059, 1049.830
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: 51491.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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) / References: UniProt: Q51487
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: 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: obtained synthetically / 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: 3.63 Å3/Da / Density % sol: 66.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 400, sodium citrate, sodium chloride, magnesium chloride.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.2→100 Å / Num. obs: 195912 / % possible obs: 98.1 % / Redundancy: 6.97 % / Rmerge(I) obs: 0.198 / Net I/σ(I): 7.59
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 1.71 / Num. unique obs: 11999

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D5K

3d5k


Resolution: 3.2→49.99 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3184 1275 4.99 %
Rwork0.2705 24288 -
obs0.2729 25563 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.51 Å2 / Biso mean: 96.5424 Å2 / Biso min: 36.32 Å2
Refinement stepCycle: final / Resolution: 3.2→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6940 0 65 0 7005
Biso mean--81.36 --
Num. residues----908
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.330.40411310.37226692800100
3.33-3.480.36931290.330326642793100
3.48-3.660.38671450.293126552800100
3.66-3.890.33991360.269827142850100
3.89-4.190.30121270.26122680280799
4.19-4.610.29091390.24062687282699
4.61-5.280.2951430.2242716285999
5.28-6.650.30721710.27672696286798
6.65-49.990.30781540.27152807296195

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