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- PDB-6f3z: Complex of E. coli LolA and periplasmic domain of LolC -

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Basic information

Entry
Database: PDB / ID: 6f3z
TitleComplex of E. coli LolA and periplasmic domain of LolC
Components
  • Lipoprotein-releasing system transmembrane protein LolC
  • Outer-membrane lipoprotein carrier protein
KeywordsPROTEIN TRANSPORT / Lipoprotein trafficking
Function / homology
Function and homology information


lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / plasma membrane protein complex / lipoprotein transport / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / plasma membrane
Similarity search - Function
Outer membrane lipoprotein carrier protein LolA, Proteobacteria / Outer membrane lipoprotein carrier protein LolA / Lipoprotein localisation LolA/LolB/LppX / Outer membrane lipoprotein carrier protein LolA-like / Lipoprotein-releasing system transmembrane protein LolC/E / outer membrane lipoprotein receptor (LolB), chain A / Lipoprotein localisation LolA/LolB/LppX / Clam / MacB-like periplasmic core domain / MacB-like periplasmic core domain ...Outer membrane lipoprotein carrier protein LolA, Proteobacteria / Outer membrane lipoprotein carrier protein LolA / Lipoprotein localisation LolA/LolB/LppX / Outer membrane lipoprotein carrier protein LolA-like / Lipoprotein-releasing system transmembrane protein LolC/E / outer membrane lipoprotein receptor (LolB), chain A / Lipoprotein localisation LolA/LolB/LppX / Clam / MacB-like periplasmic core domain / MacB-like periplasmic core domain / ABC3 transporter permease protein domain / FtsX-like permease family / Mainly Beta
Similarity search - Domain/homology
Lipoprotein-releasing system transmembrane protein LolC / Outer-membrane lipoprotein carrier protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKaplan, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N000994/1 United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Insights into bacterial lipoprotein trafficking from a structure of LolA bound to the LolC periplasmic domain.
Authors: Kaplan, E. / Greene, N.P. / Crow, A. / Koronakis, V.
History
DepositionNov 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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: Lipoprotein-releasing system transmembrane protein LolC
B: Outer-membrane lipoprotein carrier protein
C: Lipoprotein-releasing system transmembrane protein LolC
D: Outer-membrane lipoprotein carrier protein


Theoretical massNumber of molelcules
Total (without water)97,1174
Polymers97,1174
Non-polymers00
Water2,738152
1
A: Lipoprotein-releasing system transmembrane protein LolC
B: Outer-membrane lipoprotein carrier protein


Theoretical massNumber of molelcules
Total (without water)48,5582
Polymers48,5582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-9 kcal/mol
Surface area20520 Å2
MethodPISA
2
C: Lipoprotein-releasing system transmembrane protein LolC
D: Outer-membrane lipoprotein carrier protein


Theoretical massNumber of molelcules
Total (without water)48,5582
Polymers48,5582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-8 kcal/mol
Surface area20670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.010, 68.230, 94.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLUAA48 - 2711 - 224
21METMETGLUGLUCC48 - 2711 - 224
12SERSERLYSLYSBB-5 - 18219 - 206
22SERSERLYSLYSDD-5 - 18219 - 206

NCS ensembles :
ID
1
2

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Components

#1: Protein Lipoprotein-releasing system transmembrane protein LolC


Mass: 25623.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lolC, ycfU, b1116, JW5161 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ADC3
#2: Protein Outer-membrane lipoprotein carrier protein / P20


Mass: 22935.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lolA, lplA, yzzV, b0891, JW0874 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61316
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop
Details: 45% w/v Poly(acrylic acid sodium salt) 2100, 100 mM HEPES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→73.01 Å / Num. obs: 61745 / % possible obs: 95.8 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 4379 / CC1/2: 0.883 / Rsym value: 0.844 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NAA, 1IWL

5naa

1iwl


Resolution: 2→73.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.715 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 3123 5.1 %RANDOM
Rwork0.20222 ---
obs0.2046 58544 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.619 Å2
Baniso -1Baniso -2Baniso -3
1--3.21 Å2-0 Å2-0 Å2
2--0.07 Å2-0 Å2
3---3.14 Å2
Refinement stepCycle: 1 / Resolution: 2→73.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6506 0 0 152 6658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196677
X-RAY DIFFRACTIONr_bond_other_d0.0020.026004
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.9389058
X-RAY DIFFRACTIONr_angle_other_deg1.061314002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2165835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.06325.271332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.245151131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4771538
X-RAY DIFFRACTIONr_chiral_restr0.1250.2983
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217539
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021303
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_it4.3374.4053340
X-RAY DIFFRACTIONr_mcbond_other4.3364.4053339
X-RAY DIFFRACTIONr_mcangle_it6.1916.5774175
X-RAY DIFFRACTIONr_mcangle_other6.1916.5774176
X-RAY DIFFRACTIONr_scbond_it5.3194.8893336
X-RAY DIFFRACTIONr_scbond_other5.3164.893336
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9377.084883
X-RAY DIFFRACTIONr_long_range_B_refined9.94751.2357147
X-RAY DIFFRACTIONr_long_range_B_other9.95351.227132
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A13848
12C13848
21B12088
22D12088
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 243 -
Rwork0.299 4328 -
obs--96.39 %

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