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- PDB-5nsw: Xenon for tunnelling analysis of the efflux pump component OprN. -

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Basic information

Entry
Database: PDB / ID: 5nsw
TitleXenon for tunnelling analysis of the efflux pump component OprN.
ComponentsMultidrug efflux outer membrane protein OprN
KeywordsMEMBRANE PROTEIN / Efflux / Cavity / Xenon / RND pump
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
NICKEL (II) ION / PALMITIC ACID / XENON / Multidrug efflux outer membrane protein OprN
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPhan, G. / Prange, T. / Enguene Ntsogo, Y.V. / Garnier, C. / Ducruix, A. / Broutin, I.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BSV8-0010-01 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
DepositionApr 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations
Category: diffrn_radiation_wavelength / pdbx_struct_assembly ...diffrn_radiation_wavelength / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_site / struct_site_gen
Item: _struct_site.details / _struct_site.pdbx_auth_asym_id ..._struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
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.pdbx_ptnr2_label_alt_id / _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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 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: 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)153,64832
Polymers148,6263
Non-polymers5,02229
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23800 Å2
ΔGint-71 kcal/mol
Surface area57990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)256.412, 256.412, 81.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA1 - 4451 - 445
21PROPROBB1 - 4451 - 445
12GLNGLNAA1 - 4441 - 444
22GLNGLNCC1 - 4441 - 444
13GLNGLNBB1 - 4441 - 444
23GLNGLNCC1 - 4441 - 444

NCS ensembles :
ID
1
2
3

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Components

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Protein / Sugars , 2 types, 7 molecules ABC

#1: Protein Multidrug efflux outer membrane protein OprN


Mass: 49542.059 Da / Num. of mol.: 3
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.: 4
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, 553 molecules

#2: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Xe
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 100 mM sodium acetate, 1 M sodium formate, 10 % PEG 4000 (w/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.771 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.771 Å / Relative weight: 1
ReflectionResolution: 2.5→181 Å / Num. obs: 91716 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.07 / Net I/σ(I): 4.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IUY

5iuy


Resolution: 2.5→49.42 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.898 / SU B: 15.254 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R Free: 0.218 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23938 4736 5.2 %RANDOM
Rwork0.17133 ---
obs0.17491 86977 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.791 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Resolution: 2.5→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10311 0 198 528 11037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01910748
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210214
X-RAY DIFFRACTIONr_angle_refined_deg2.1761.9814504
X-RAY DIFFRACTIONr_angle_other_deg1.132323538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2651360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19722.868537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.54151763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4415149
X-RAY DIFFRACTIONr_chiral_restr0.1040.21612
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022296
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_it5.7373.8265395
X-RAY DIFFRACTIONr_mcbond_other5.7123.8265394
X-RAY DIFFRACTIONr_mcangle_it6.9415.7266749
X-RAY DIFFRACTIONr_mcangle_other6.9495.7276750
X-RAY DIFFRACTIONr_scbond_it7.6864.4095353
X-RAY DIFFRACTIONr_scbond_other7.6854.4095354
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.6846.367749
X-RAY DIFFRACTIONr_long_range_B_refined7.69644.94412051
X-RAY DIFFRACTIONr_long_range_B_other7.66244.88711988
X-RAY DIFFRACTIONr_rigid_bond_restr7.113320962
X-RAY DIFFRACTIONr_sphericity_free30.385389
X-RAY DIFFRACTIONr_sphericity_bonded15.522520958
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A279260.09
12B279260.09
21A276460.09
22C276460.09
31B272860.1
32C272860.1
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 318 -
Rwork0.196 6426 -
obs--99.93 %

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