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

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Basic information

Entry
Database: PDB / ID: 5nuq
TitleStructural basis for maintenance of bacterial outer membrane lipid asymmetry
Components
  • Outer membrane protein F
  • Probable phospholipid-binding lipoprotein mlaA
KeywordsMEMBRANE PROTEIN / Outer membrane / lipid asymmetry / lipoprotein / phospholipid translocation
Function / homology
Function and homology information


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 ...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
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 ...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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Serratia marcescens (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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein F
B: Outer membrane protein F
C: Outer membrane protein F
D: Outer membrane protein F
E: Outer membrane protein F
F: Outer membrane protein F
G: Probable phospholipid-binding lipoprotein mlaA
H: Probable phospholipid-binding lipoprotein mlaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,04217
Polymers275,2848
Non-polymers2,7589
Water00
1
A: Outer membrane protein F
C: Outer membrane protein F
E: Outer membrane protein F
H: Probable phospholipid-binding lipoprotein mlaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,8688
Polymers137,6424
Non-polymers1,2264
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer membrane protein F
D: Outer membrane protein F
F: Outer membrane protein F
G: Probable phospholipid-binding lipoprotein mlaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,1749
Polymers137,6424
Non-polymers1,5325
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.491, 163.039, 230.740
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.: 6
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 Probable phospholipid-binding lipoprotein mlaA


Mass: 26299.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: mlaA, ERS381432_02710 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U8E5M0
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM

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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: 3.95 Å3/Da / Density % sol: 68.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.32 M lithium chloride 0.1M Sodium citrate pH 5.5 and 14% 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 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionResolution: 3.2→94.242 Å / Num. obs: 72631 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.985 / Rpim(I) all: 0.148 / Net I/σ(I): 4.5
Reflection shellResolution: 3.2→3.27 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4398 / CC1/2: 0.724 / Rpim(I) all: 0.494 / % possible all: 100

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Processing

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

2zfg


Resolution: 3.2→94.242 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.39
RfactorNum. reflection% reflection
Rfree0.3065 5662 7.82 %
Rwork0.2383 --
obs0.2436 72392 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→94.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18952 0 100 0 19052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819472
X-RAY DIFFRACTIONf_angle_d1.30226317
X-RAY DIFFRACTIONf_dihedral_angle_d7.05511115
X-RAY DIFFRACTIONf_chiral_restr0.0632660
X-RAY DIFFRACTIONf_plane_restr0.0083531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.23640.40432140.33652132X-RAY DIFFRACTION100
3.2364-3.27440.39562040.32742202X-RAY DIFFRACTION100
3.2744-3.31440.32891800.31432199X-RAY DIFFRACTION100
3.3144-3.35630.41821820.28352190X-RAY DIFFRACTION100
3.3563-3.40050.35691940.26582226X-RAY DIFFRACTION100
3.4005-3.44710.29841890.26212194X-RAY DIFFRACTION100
3.4471-3.49630.32951960.26932200X-RAY DIFFRACTION100
3.4963-3.54850.31181640.2742217X-RAY DIFFRACTION100
3.5485-3.6040.34271930.27792189X-RAY DIFFRACTION100
3.604-3.66310.32861790.26962190X-RAY DIFFRACTION100
3.6631-3.72620.35051880.24422230X-RAY DIFFRACTION100
3.7262-3.7940.34851860.24642172X-RAY DIFFRACTION100
3.794-3.8670.35131840.24892236X-RAY DIFFRACTION100
3.867-3.94590.31681840.24142180X-RAY DIFFRACTION100
3.9459-4.03170.29081810.22912223X-RAY DIFFRACTION100
4.0317-4.12550.33361980.23152213X-RAY DIFFRACTION100
4.1255-4.22870.31422000.22372201X-RAY DIFFRACTION100
4.2287-4.3430.31141660.21162239X-RAY DIFFRACTION100
4.343-4.47080.26861680.21632229X-RAY DIFFRACTION100
4.4708-4.61510.26531880.21552255X-RAY DIFFRACTION100
4.6151-4.780.26111870.21032203X-RAY DIFFRACTION100
4.78-4.97140.2821880.20992222X-RAY DIFFRACTION100
4.9714-5.19760.27312100.21112214X-RAY DIFFRACTION100
5.1976-5.47160.28281930.20142251X-RAY DIFFRACTION100
5.4716-5.81440.26481880.21572238X-RAY DIFFRACTION100
5.8144-6.26330.26991970.21142242X-RAY DIFFRACTION100
6.2633-6.89340.25791820.20532289X-RAY DIFFRACTION100
6.8934-7.89040.2921770.20482263X-RAY DIFFRACTION100
7.8904-9.93940.24261980.19462302X-RAY DIFFRACTION100
9.9394-94.2830.27622040.24982389X-RAY DIFFRACTION98
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)
11.0223-0.2026-0.26811.214-0.26881.3107-0.08090.1363-0.067-0.00170.064-0.16750.02210.03640.02070.4032-0.04540.05130.2549-0.04480.2294-25.4579-21.04464.6819
20.6365-0.2240.11470.7544-0.44211.2128-0.1364-0.1160.1470.16990.02630.07320.03040.03750.09230.4716-0.0268-0.01310.2401-0.08670.2874-26.2191-59.819530.2614
31.3366-0.58770.11811.57990.30220.8642-0.1397-0.16180.12130.3060.1015-0.21280.13540.2040.03090.5234-0.0988-0.03050.3184-0.05760.2256-20.0226-5.619239.3918
41.2936-0.1211-0.42671.0284-0.05620.2748-0.04680.287-0.0314-0.2306-0.0510.0597-0.0255-0.04530.09880.4497-0.0539-0.05330.3606-0.0210.173-20.6939-75.5257-4.3736
50.5271-0.10550.29270.40250.08380.8377-0.09510.09530.34660.17030.014-0.2221-0.66420.30950.02940.7771-0.14570.14280.27550.03510.4303-20.268716.748.0841
60.6627-0.0815-0.28230.93590.03760.4773-0.2337-0.0733-0.32610.1508-0.00930.05670.4707-0.02540.1320.7072-0.06140.13160.2644-0.00510.3501-21.7535-97.717826.8859
70.42710.29550.25120.5218-0.23160.7772-0.4277-0.3787-0.16090.27180.05030.02350.1528-0.27450.18940.76570.09440.2410.55840.0550.3343-42.0482-85.629868.8215
80.2118-0.41110.35421.1633-0.00972.4892-0.05480.20250.1066-0.5467-0.2621-0.0519-0.19220.00850.27720.4949-0.08120.02810.44720.07580.3401-41.08244.6151-33.8766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 340)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 340)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 340)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 340)
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 340)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 340)
7X-RAY DIFFRACTION7(chain 'G' and resid 11 through 210)
8X-RAY DIFFRACTION8(chain 'H' and resid 12 through 210)

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