[English] 日本語
Yorodumi
- PDB-7zax: Solution structure of thanatin-like derivative 7 in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zax
TitleSolution structure of thanatin-like derivative 7 in complex with K. pneumoniae LptA
Components
  • Lipopolysaccharide export system protein LptA
  • Thanatin-like derivative
KeywordsANTIBIOTIC / STRUCTURE FROM CYANA 3.98.13
Function / homology
Function and homology information


lipopolysaccharide transmembrane transporter activity / glycolipid transfer activity / Gram-negative-bacterium-type cell outer membrane assembly / defense response to fungus / lipopolysaccharide binding / outer membrane-bounded periplasmic space / killing of cells of another organism / defense response to bacterium / innate immune response / extracellular region / plasma membrane
Similarity search - Function
Lipopolysaccharide assembly, LptC-related / Lipopolysaccharide export system protein LptC / : / Lipopolysaccharide-assembly, LptC-related / Lipopolysaccharide export system protein LptA / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein
Similarity search - Domain/homology
Multifunctional fusion protein / Thanatin
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
Podisus maculiventris (spined soldier bug)
MethodSOLUTION NMR / molecular dynamics
AuthorsOi, K.K. / Moehle, K. / Zerbe, O.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
Innosuisse33285.1 IP-LSEuropean Union
CitationJournal: Sci Adv / Year: 2023
Title: Peptidomimetic antibiotics disrupt the lipopolysaccharide transport bridge of drug-resistant Enterobacteriaceae.
Authors: Schuster, M. / Brabet, E. / Oi, K.K. / Desjonqueres, N. / Moehle, K. / Le Poupon, K. / Hell, S. / Gable, S. / Rithie, V. / Dillinger, S. / Zbinden, P. / Luther, A. / Li, C. / Stiegeler, S. / ...Authors: Schuster, M. / Brabet, E. / Oi, K.K. / Desjonqueres, N. / Moehle, K. / Le Poupon, K. / Hell, S. / Gable, S. / Rithie, V. / Dillinger, S. / Zbinden, P. / Luther, A. / Li, C. / Stiegeler, S. / D'Arco, C. / Locher, H. / Remus, T. / DiMaio, S. / Motta, P. / Wach, A. / Jung, F. / Upert, G. / Obrecht, D. / Benghezal, M. / Zerbe, O.
History
DepositionMar 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 2.0Jun 14, 2023Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_mod_residue / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _pdbx_entity_src_syn.organism_common_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipopolysaccharide export system protein LptA
B: Thanatin-like derivative


Theoretical massNumber of molelcules
Total (without water)16,7982
Polymers16,7982
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1target function

-
Components

#1: Protein Lipopolysaccharide export system protein LptA


Mass: 14790.585 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: lptC, lptA, NCTC9128_02683 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A2X3CC60
#2: Protein/peptide Thanatin-like derivative


Mass: 2007.387 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: VAN = HYP = hydroxyproline PEN = penicillamine DAB = diaminobutyric acid DDA = D-DAB
Source: (synth.) Podisus maculiventris (spined soldier bug) / References: UniProt: P55788
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HN(COCA)CB
161isotropic13D HN(CA)CB
171isotropic13D 1H-13C NOESY aliphatic
181isotropic13D 1H-13C NOESY aromatic
191isotropic13D 1H-15N NOESY
1101isotropic13D HBHA(CO)NH
1111isotropic23D (H)CCH-TOCSY

-
Sample preparation

DetailsType: solution
Contents: 300 uM [U-13C; U-15N] Lipopolysaccharide export system protein LptA, 50 mM sodium phosphate, 150 mM NaCl, 500 uM Thanatin-like derivative 4, 90% H2O/10% D2O
Details: 13C,15N-labelled LptA(28-145) / Label: LptAm_15N13C / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMLipopolysaccharide export system protein LptA[U-13C; U-15N]1
50 mMsodium phosphatenone1
150 mMNaClnone1
500 uMThanatin-like derivative 4none1
Sample conditionsIonic strength: 150 mM / Ionic strength err: 10 / Label: conditions_1 / pH: 7 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO7001
Bruker AVANCE NEOBrukerAVANCE NEO6002

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98Gunthert, Mumenthaler and Wuthrichstructure calculation
MOE2020.09Chemical Computing Group ULC, 1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7, 2022refinement
CARAKeller and Wuthrichchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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