[English] 日本語
Yorodumi
- PDB-6f49: Periplasmic domain of LolC lacking the Hook. -

+
Open data


ID or keywords:

Loading...

-
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 C-terminal
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

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

-
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


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


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


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more