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- PDB-5nuo: Structural basis for maintenance of bacterial outer membrane lipi... -

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Basic information

Entry
Database: PDB / ID: 5nuo
TitleStructural basis for maintenance of bacterial outer membrane lipid asymmetry
Components
  • ABC transporter permease
  • Outer membrane protein F
KeywordsMEMBRANE PROTEIN / Outer membrane / lipid asymmetry / lipoprotein / phospholipid translocation
Function / homology
Function and homology information


intermembrane phospholipid transfer / colicin transmembrane transporter activity / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / monoatomic ion channel complex / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding ...intermembrane phospholipid transfer / colicin transmembrane transporter activity / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / monoatomic ion channel complex / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding / protein transport / monoatomic ion transmembrane transport / lipid binding / identical protein binding / membrane
Similarity search - Function
MlaA lipoprotein / MlaA lipoprotein / 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 / : ...MlaA lipoprotein / MlaA lipoprotein / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ABC transporter permease / Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Klebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsAbellon-Ruiz, J. / Kaptan, S.S. / Basle, A. / Claudi, B. / Bumann, D. / Kleinekathofer, U. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Union115525 United Kingdom
CitationJournal: Nat Microbiol / Year: 2017
Title: Structural basis for maintenance of bacterial outer membrane lipid asymmetry.
Authors: Abellon-Ruiz, J. / Kaptan, S.S. / Basle, A. / Claudi, B. / Bumann, D. / Kleinekathofer, U. / van den Berg, B.
History
DepositionMay 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 6, 2017Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Outer membrane protein F
D: ABC transporter permease
A: Outer membrane protein F
B: ABC transporter permease
E: Outer membrane protein F
F: ABC transporter permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,14132
Polymers190,4366
Non-polymers6,70526
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26670 Å2
ΔGint-159 kcal/mol
Surface area67200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.597, 146.461, 234.931
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Outer membrane protein F / Outer membrane protein 1A / Outer membrane protein B / Outer membrane protein IA / Porin OmpF


Mass: 37114.250 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ompF, cmlB, coa, cry, tolF, b0929, JW0912 / Production host: Escherichia coli (E. coli) / References: UniProt: P02931
#2: Protein ABC transporter permease / Lipoprotein / Phospholipid-binding lipoprotein MlaA / Putative phospholipid-binding lipoprotein ...Lipoprotein / Phospholipid-binding lipoprotein MlaA / Putative phospholipid-binding lipoprotein MlaA / VacJ protein


Mass: 26364.527 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: mlaA, vacJ, AGG09_21815, BB749_07690, BCB67_11070, BL143_09030, BN49_3944, PMK1_00224, SAMEA3531778_01593, SM30_03044, SM57_02930
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W8AQT6
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
Has protein modificationN

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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: 4.32 Å3/Da / Density % sol: 71.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.05 M sodium sulfate, 0.05 M lithium sulfate, 0.05 M Tris pH 8.5 and 35 % PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97886 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionResolution: 3.07→95.6 Å / Num. obs: 62533 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rpim(I) all: 0.048 / Net I/σ(I): 8.5
Reflection shellResolution: 3.07→3.12 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2880 / CC1/2: 0.895 / Rpim(I) all: 0.425 / % possible all: 92.9

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Processing

Software
NameVersionClassification
DIALSdata reduction
xia2data reduction
Aimlessdata scaling
PHASERphasing
PHENIX(1.11.1_2575: ???)refinement
RESOLVEmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZFG

2zfg


Resolution: 3.2→88.547 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.19
RfactorNum. reflection% reflection
Rfree0.2693 2538 5.01 %
Rwork0.2228 --
obs0.2251 50693 91.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→88.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12659 0 312 0 12971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113264
X-RAY DIFFRACTIONf_angle_d1.31217874
X-RAY DIFFRACTIONf_dihedral_angle_d8.8637630
X-RAY DIFFRACTIONf_chiral_restr0.0681786
X-RAY DIFFRACTIONf_plane_restr0.012359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.26160.36671230.32182223X-RAY DIFFRACTION78
3.2616-3.32810.37941130.2932270X-RAY DIFFRACTION79
3.3281-3.40050.31891170.26022386X-RAY DIFFRACTION82
3.4005-3.47960.31851340.26962428X-RAY DIFFRACTION85
3.4796-3.56660.30821450.25392524X-RAY DIFFRACTION87
3.5666-3.66310.29371480.2492512X-RAY DIFFRACTION88
3.6631-3.77080.34111540.24062544X-RAY DIFFRACTION90
3.7708-3.89260.23741300.21852650X-RAY DIFFRACTION91
3.8926-4.03170.22711390.21322671X-RAY DIFFRACTION93
4.0317-4.19310.24251340.20772743X-RAY DIFFRACTION94
4.1931-4.38390.22881490.19242791X-RAY DIFFRACTION96
4.3839-4.61510.23791540.17562815X-RAY DIFFRACTION97
4.6151-4.90420.23861420.17942818X-RAY DIFFRACTION97
4.9042-5.28280.24171510.18352872X-RAY DIFFRACTION98
5.2828-5.81430.26071360.19282901X-RAY DIFFRACTION99
5.8143-6.65540.24011650.19852917X-RAY DIFFRACTION99
6.6554-8.38410.26561430.21752984X-RAY DIFFRACTION99
8.3841-88.5810.261610.25323106X-RAY DIFFRACTION99
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)
10.5894-0.09160.26930.54620.06260.1712-0.2823-0.06140.24070.40760.0830.567-0.1829-0.0053-1.1506-0.02870.07450.28180.1723-0.02150.4173-30.63138.7118-60.4564
20.3686-0.08170.45020.033-0.15540.709-0.0255-0.1461-0.2070.40770.19670.06960.12110.0776-0.09420.5860.20090.02020.38730.04060.2718-10.217210.9721-26.8597
30.4819-0.0952-0.0360.2349-0.02071.4617-0.10680.0249-0.24010.1620.21270.46390.71290.09210.31290.19050.02430.09740.12930.04190.4258-30.21841.669-70.1647
40.258-0.1651-0.0941.16370.53070.24330.27210.3473-0.1017-0.08690.1518-0.42070.51230.6324-0.19340.82890.23-0.05220.7046-0.18710.417-20.2811-14.0959-114.4
50.26960.06380.06870.74990.02270.0629-0.15080.42820.1654-0.74240.07250.6334-0.0397-0.0766-0.07010.1885-0.1546-0.27610.45830.09470.4758-35.030328.5416-97.1014
60.59750.4354-0.46220.6633-0.60260.9871-0.02420.06980.3909-0.2450.28070.7169-0.3565-0.1525-0.18420.5457-0.1539-0.14420.41910.19190.6408-20.3274.2925-92.5087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'C' and resid 1 through 340)
2X-RAY DIFFRACTION2(chain 'D' and resid 12 through 211)
3X-RAY DIFFRACTION3(chain 'A' and resid 1 through 340)
4X-RAY DIFFRACTION4(chain 'B' and resid 15 through 211)
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 340)
6X-RAY DIFFRACTION6(chain 'F' and resid 13 through 211)

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