[English] 日本語
Yorodumi
- PDB-6s10: NMR solution structure of a ProQ homolog from Legionella pneumophila -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s10
TitleNMR solution structure of a ProQ homolog from Legionella pneumophila
ComponentsRNA chaperone ProQ
KeywordsRNA BINDING PROTEIN / ProQ / sRNA
Function / homology
Function and homology information


RNA strand-exchange activity / RNA strand annealing activity / post-transcriptional regulation of gene expression / cytoplasm
Similarity search - Function
RNA chaperone ProQ / ProQ/FinO domain superfamily / ProQ/FINO family / ProQ/FinO domain / ProQ/FINO family
Similarity search - Domain/homology
ProQ-like, activator of ProP osmoprotectant transporter / ProQ-like, activator of ProP osmoprotectant transporter
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsImmer, C. / Hacker, C. / Woehnert, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC902 Germany
CitationJournal: Rna / Year: 2020
Title: Solution structure and RNA-binding of a minimal ProQ-homolog from Legionella pneumophila (Lpp1663).
Authors: Immer, C. / Hacker, C. / Wohnert, J.
History
DepositionJun 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 25, 2020Group: 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 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA chaperone ProQ


Theoretical massNumber of molelcules
Total (without water)14,1711
Polymers14,1711
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9470 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein RNA chaperone ProQ


Mass: 14170.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: proQ_1, proQ_2, ERS240541_00599, NCTC12024_01603 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A131MWN1, UniProt: Q5ZUU4*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic32D 1H-13C HSQC aromatic
132isotropic13D HNCO
142isotropic13D HCACO
152isotropic13D HN(CA)CB
162isotropic13D HBHA(CO)NH
172isotropic13D (H)CCH-TOCSY
182isotropic13D H(CCO)NH
192isotropic13D C(CO)NH
1101isotropic23D 1H-15N NOESY
1112isotropic33D 1H-13C NOESY aliphatic
1122isotropic33D 1H-13C NOESY aromatic
1132isotropic32D 1H-13C HSQC aliphatic
1143isotropic12D 1H-15N HSQC
1154isotropic12D 1H-15N HSQC
1165isotropic12D 1H-15N HSQC
1175isotropic12D 1H-13C HSQC aliphatic
1186isotropic13D 1H-13C NOESY aliphatic

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1400 uM [U-15N] Lpp1663, 50 mM sodium phosphate, 100 mM sodium chloride, 2 mM beta-mercaptoethanol, 50 uM DSS, 90% H2O/10% D2O15N_Lpp166390% H2O/10% D2O
solution2400 uM [U-13C; U-15N] Lpp1663, 50 mM sodium phosphate, 100 mM sodium chloride, 2 mM beta-mercaptoethanol, 50 uM DSS, 90% H2O/10% D2O13C15N_Lpp166390% H2O/10% D2O
solution3400 uM [U-15N]-Lys Lpp1663, 50 mM sodium phosphate, 100 mM sodium chloride, 2 mM beta-mercaptoethanol, 50 uM DSS, 90% H2O/10% D2O15N_Lys90% H2O/10% D2O
solution4400 uM [U-15N]-Tyr Lpp1663, 50 mM sodium phosphate, 100 mM sodium chloride, 2 mM beta-mercaptoethanol, 50 uM DSS, 90% H2O/10% D2O15N_Tyr90% H2O/10% D2O
solution5400 uM [U-15N]-Phe; [U-13C]-Pro Lpp1663, 50 mM sodium phosphate, 100 mM sodium chloride, 2 mM beta-mercaptoethanol, 50 uM DSS, 90% H2O/10% D2O15N_Phe_13C_Pro90% H2O/10% D2O
solution6400 uM [U-13C; U-15N] Lpp1663, 50 mM sodium phosphate, 100 mM sodium chloride, 2 mM beta-mercaptoethanol, 50 uM DSS, 100% D2O13C_15N_Lpp1663_D20100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMLpp1663[U-15N]1
50 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
2 mMbeta-mercaptoethanolnatural abundance1
50 uMDSSnatural abundance1
400 uMLpp1663[U-13C; U-15N]2
50 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
2 mMbeta-mercaptoethanolnatural abundance2
50 uMDSSnatural abundance2
400 uMLpp1663[U-15N]-Lys3
50 mMsodium phosphatenatural abundance3
100 mMsodium chloridenatural abundance3
2 mMbeta-mercaptoethanolnatural abundance3
50 uMDSSnatural abundance3
400 uMLpp1663[U-15N]-Tyr4
50 mMsodium phosphatenatural abundance4
100 mMsodium chloridenatural abundance4
2 mMbeta-mercaptoethanolnatural abundance4
50 uMDSSnatural abundance4
400 uMLpp1663[U-15N]-Phe; [U-13C]-Pro5
50 mMsodium phosphatenatural abundance5
100 mMsodium chloridenatural abundance5
2 mMbeta-mercaptoethanolnatural abundance5
50 uMDSSnatural abundance5
400 uMLpp1663[U-13C; U-15N]6
50 mMsodium phosphatenatural abundance6
100 mMsodium chloridenatural abundance6
2 mMbeta-mercaptoethanolnatural abundance6
50 uMDSSnatural abundance6
Sample conditionsIonic strength: 100 mM / Label: conditions / pH: 6.5 / Pressure: AMBIENT atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCEBrukerAVANCE8003

-
Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
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