[English] 日本語
Yorodumi
- PDB-6mit: LptBFGC from Enterobacter cloacae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mit
TitleLptBFGC from Enterobacter cloacae
Components
  • (Lipopolysaccharide export system ...) x 3
  • LPS export ABC transporter permease LptF
KeywordsLIPID TRANSPORT / lipopolysaccharide transport / ABC-transporter
Function / homology
Function and homology information


lipopolysaccharide transmembrane transporter activity / Gram-negative-bacterium-type cell outer membrane assembly / plasma membrane => GO:0005886 / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Lipopolysaccharide assembly, LptC-related / Lipopolysaccharide export system protein LptC / Lipopolysaccharide-assembly, LptC-related / Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG / Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB ...Lipopolysaccharide assembly, LptC-related / Lipopolysaccharide export system protein LptC / Lipopolysaccharide-assembly, LptC-related / Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG / Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NOVOBIOCIN / Lipopolysaccharide export system permease protein LptG / Lipopolysaccharide export system ATP-binding protein LptB / Lipopolysaccharide export system protein LptC / Lipopolysaccharide export system permease protein LptF / Lipopolysaccharide export system permease protein LptF
Similarity search - Component
Biological speciesEnterobacter cloacae subsp. cloacae (bacteria)
Enterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsOwens, T.W. / Kahne, D. / Kruse, A.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 GM066174 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI081059 United States
CitationJournal: Nature / Year: 2019
Title: Structural basis of unidirectional export of lipopolysaccharide to the cell surface.
Authors: Owens, T.W. / Taylor, R.J. / Pahil, K.S. / Bertani, B.R. / Ruiz, N. / Kruse, A.C. / Kahne, D.
History
DepositionSep 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 21, 2020Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rpim_I_all
Revision 1.5Oct 11, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipopolysaccharide export system ATP-binding protein
B: Lipopolysaccharide export system ATP-binding protein
C: Lipopolysaccharide export system protein LptC
F: LPS export ABC transporter permease LptF
G: Lipopolysaccharide export system permease protein LptG
D: Lipopolysaccharide export system ATP-binding protein
E: Lipopolysaccharide export system ATP-binding protein
H: Lipopolysaccharide export system protein LptC
I: LPS export ABC transporter permease LptF
J: Lipopolysaccharide export system permease protein LptG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,79223
Polymers312,08710
Non-polymers1,70513
Water1448
1
A: Lipopolysaccharide export system ATP-binding protein
B: Lipopolysaccharide export system ATP-binding protein
C: Lipopolysaccharide export system protein LptC
F: LPS export ABC transporter permease LptF
G: Lipopolysaccharide export system permease protein LptG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,75113
Polymers156,0435
Non-polymers7088
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13170 Å2
ΔGint-195 kcal/mol
Surface area61590 Å2
MethodPISA
2
D: Lipopolysaccharide export system ATP-binding protein
E: Lipopolysaccharide export system ATP-binding protein
H: Lipopolysaccharide export system protein LptC
I: LPS export ABC transporter permease LptF
J: Lipopolysaccharide export system permease protein LptG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,04010
Polymers156,0435
Non-polymers9975
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11030 Å2
ΔGint-151 kcal/mol
Surface area61380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.427, 156.984, 295.518
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

-
Components

-
Lipopolysaccharide export system ... , 3 types, 8 molecules ABDECHGJ

#1: Protein
Lipopolysaccharide export system ATP-binding protein


Mass: 26819.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56) (bacteria)
Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: ECL_04583 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3CR83
#2: Protein Lipopolysaccharide export system protein LptC


Mass: 22255.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56) (bacteria)
Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: lptC, ECL_04581 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3CU18
#4: Protein Lipopolysaccharide export system permease protein LptG


Mass: 39566.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56) (bacteria)
Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: ECL_04592 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3CQA2

-
Protein , 1 types, 2 molecules FI

#3: Protein LPS export ABC transporter permease LptF / Lipopolysaccharide export system permease protein lptF


Mass: 40582.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: lptF, CP904_11410, ERS370009_01510 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A232G4N0, UniProt: A0A421IFY4*PLUS

-
Non-polymers , 4 types, 21 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#7: Chemical ChemComp-NOV / NOVOBIOCIN / 4-Hydroxy-3-[4-hydroxy-3-(3-methylbut-2-enyl)benzamido]-8-methylcoumarin-7-yl 3-O-carbamoyl-5,5-di-C-methyl-alpha-l-lyxofuranoside


Mass: 612.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C31H36N2O11 / Comment: antibiotic*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.33 Å3/Da / Density % sol: 71.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 21% PEG 400, 100mM MES pH 6.5, 500mM Li2SO4, 2mM Na-novobiocin

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03324 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03324 Å / Relative weight: 1
ReflectionResolution: 3→49.33 Å / Num. obs: 109124 / % possible obs: 100 % / Redundancy: 16 % / CC1/2: 0.723 / Rmerge(I) obs: 0.48 / Rpim(I) all: 0.13 / Rrim(I) all: 0.499 / Net I/σ(I): 5.6 / Num. measured all: 1745941 / Scaling rejects: 2870
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs% possible allRmerge(I) obsRpim(I) all
3-3.0512.26499153370.13786.5920.299.7
16.43-49.3315.9118067440.9980.0982096.10.0950.024

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.2 Å49.33 Å
Translation3.2 Å49.33 Å

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.1data scaling
PHASER2.8.1phasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5l75

5l75


Resolution: 3.2→49.326 Å / SU ML: 0.8 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 42.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3201 1641 1.83 %
Rwork0.279 87828 -
obs0.2798 89469 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 239.34 Å2 / Biso mean: 136.5073 Å2 / Biso min: 67.8 Å2
Refinement stepCycle: final / Resolution: 3.2→49.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19625 0 100 8 19733
Biso mean--142.68 103.63 -
Num. residues----2657
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.29410.5251240.5436718684293
3.2941-3.40040.45341370.423372887425100
3.4004-3.52190.41011360.364772787414100
3.5219-3.66290.3941350.327172637398100
3.6629-3.82960.31511380.300973067444100
3.8296-4.03140.33491370.271473217458100
4.0314-4.28380.30721360.255373177453100
4.2838-4.61440.28681380.236773427480100
4.6144-5.07830.24821370.233873767513100
5.0783-5.81210.34471380.279474157553100
5.8121-7.31890.34351400.307974677607100
7.3189-49.3320.29661450.254777377882100

+
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://pdbjlvh1.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