[English] 日本語
Yorodumi
- PDB-5lfi: lactococcin A immunity protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lfi
Titlelactococcin A immunity protein
ComponentsLactococcin-A immunity protein
KeywordsIMMUNE SYSTEM / Four-helix bundle / immunity protein / bacteriocin receptor
Function / homologyLactococcin-A immunity protein-like / Enterocin A Immunity / bacteriocin immunity / Lactococcin-A immunity protein
Function and homology information
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsPersson, C. / Fuochi, V. / Pedersen, A. / Karlsson, B.G. / Nissen-Meyer, J. / Kristiansen, P.E. / Oppegard, C.
CitationJournal: Biochemistry / Year: 2016
Title: Nuclear Magnetic Resonance Structure and Mutational Analysis of the Lactococcin A Immunity Protein.
Authors: Kristiansen, P.E. / Persson, C. / Fuochi, V. / Pedersen, A. / Karlsson, G.B. / Nissen-Meyer, J. / Oppegard, C.
History
DepositionJul 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lactococcin-A immunity protein


Theoretical massNumber of molelcules
Total (without water)13,2731
Polymers13,2731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8620 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Lactococcin-A immunity protein


Mass: 13273.202 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Gene: lciA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3M7

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic13D HNCA
131isotropic13D HN(CA)CB
141isotropic13D HN(CO)CA
151isotropic13D HN(COCA)CB
161isotropic13D HN(CA)CO
171isotropic13D 1H-15N NOESY
181isotropic13D 1H-15N TOCSY
191isotropic13D (H)CCH-TOCSY
1101isotropic13D 1H-13C NOESY aliphatic
1111isotropic13D 1H-13C NOESY aromatic
1121isotropic12D 1H-15N HSQC
1131isotropic12D 1H-13C HSQC aliphatic
1141isotropic12D 1H-13C HSQC aromatic

-
Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-100% 13C; U-100% 15N] lactococcin A immunity protein, 90% H2O/10% D2O
Label: 13C/15N / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: lactococcin A immunity protein / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.4 M / Label: Conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

-
Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 16

+
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