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- PDB-6f49: Periplasmic domain of LolC lacking the Hook. -

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Basic information

Entry
Database: PDB / ID: 6f49
TitlePeriplasmic domain of LolC lacking the Hook.
ComponentsLipoprotein-releasing system transmembrane protein LolC,Lipoprotein-releasing system transmembrane protein LolC
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
Lipoprotein-releasing system transmembrane protein LolC/E / MacB-like periplasmic core domain / MacB-like periplasmic core domain / ABC3 transporter permease protein domain / FtsX-like permease family
Similarity search - Domain/homology
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Lipoprotein-releasing system transmembrane protein LolC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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,Lipoprotein-releasing system transmembrane protein LolC
B: Lipoprotein-releasing system transmembrane protein LolC,Lipoprotein-releasing system transmembrane protein LolC
C: Lipoprotein-releasing system transmembrane protein LolC,Lipoprotein-releasing system transmembrane protein LolC
D: Lipoprotein-releasing system transmembrane protein LolC,Lipoprotein-releasing system transmembrane protein LolC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,79616
Polymers97,5194
Non-polymers1,27712
Water8,143452
1
A: Lipoprotein-releasing system transmembrane protein LolC,Lipoprotein-releasing system transmembrane protein LolC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4722
Polymers24,3801
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipoprotein-releasing system transmembrane protein LolC,Lipoprotein-releasing system transmembrane protein LolC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8345
Polymers24,3801
Non-polymers4554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lipoprotein-releasing system transmembrane protein LolC,Lipoprotein-releasing system transmembrane protein LolC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8345
Polymers24,3801
Non-polymers4554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipoprotein-releasing system transmembrane protein LolC,Lipoprotein-releasing system transmembrane protein LolC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6564
Polymers24,3801
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.310, 108.540, 109.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA48 - 2651 - 207
21ASNASNBB48 - 2651 - 207
12ASNASNAA48 - 2651 - 207
22ASNASNCC48 - 2651 - 207
13ASNASNAA48 - 2651 - 207
23ASNASNDD48 - 2651 - 207
14METMETBB48 - 2661 - 208
24METMETCC48 - 2661 - 208
15METMETBB48 - 2661 - 208
25METMETDD48 - 2661 - 208
16LEULEUCC48 - 2701 - 212
26LEULEUDD48 - 2701 - 212

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Lipoprotein-releasing system transmembrane protein LolC,Lipoprotein-releasing system transmembrane protein LolC


Mass: 24379.670 Da / Num. of mol.: 4
Mutation: delta[169-179], P167G, S168A,delta[169-179], P167G, S168A,delta[169-179], P167G, S168A,delta[169-179], P167G, S168A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Escherichia coli (E. coli)
Strain: K12 / Gene: lolC, ycfU, b1116, JW5161 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ADC3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Triethylene glycol dimethyl ether


Mass: 178.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.15 M sodium acetate pH 4.6, 30% w/v PEG 2000 MME

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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: 2.02→62.04 Å / Num. obs: 58914 / % possible obs: 99.1 % / Redundancy: 5 % / Biso Wilson estimate: 41.1 Å2 / Rsym value: 0.166 / Net I/σ(I): 6.7
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4321 / CC1/2: 0.704 / Rsym value: 0.684 / % possible all: 99.5

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Processing

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

5naa


Resolution: 2.02→62.04 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.131 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.172 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23279 2979 5.1 %RANDOM
Rwork0.18839 ---
obs0.19061 55872 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.774 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0 Å20 Å2
2--2.18 Å2-0 Å2
3----1.08 Å2
Refinement stepCycle: 1 / Resolution: 2.02→62.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6527 0 84 452 7063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196829
X-RAY DIFFRACTIONr_bond_other_d0.0030.026438
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9779239
X-RAY DIFFRACTIONr_angle_other_deg1.009314974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2455859
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56425.247324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.003151205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4941551
X-RAY DIFFRACTIONr_chiral_restr0.0960.21029
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217620
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021267
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_it1.962.0783418
X-RAY DIFFRACTIONr_mcbond_other1.9582.0773417
X-RAY DIFFRACTIONr_mcangle_it3.0033.1014283
X-RAY DIFFRACTIONr_mcangle_other3.0023.1024284
X-RAY DIFFRACTIONr_scbond_it2.892.4673411
X-RAY DIFFRACTIONr_scbond_other2.892.4673411
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5093.5334957
X-RAY DIFFRACTIONr_long_range_B_refined6.19624.9477517
X-RAY DIFFRACTIONr_long_range_B_other6.16324.8147435
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 / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A131240.07
12B131240.07
21A131160.07
22C131160.07
31A131240.07
32D131240.07
41B133080.07
42C133080.07
51B133720.07
52D133720.07
61C135140.08
62D135140.08
LS refinement shellResolution: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 209 -
Rwork0.27 4106 -
obs--99.47 %

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