[English] 日本語
Yorodumi
- PDB-6yse: Gp4 from the Pseudomonas phage LUZ24 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yse
TitleGp4 from the Pseudomonas phage LUZ24
ComponentsGp4
KeywordsPEPTIDE BINDING PROTEIN / Gp4 / phage / antimicrobial / Pseudomonas
Function / homologyUncharacterized protein gp4
Function and homology information
Biological speciesPseudomonas phage LUZ24 (virus)
MethodSOLUTION NMR / simulated annealing / torsion angle dynamics
AuthorsBdira, F.B. / Volkov, A.N. / Dame, R.T.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)VICI 016.160.613 Netherlands
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Novel anti-repression mechanism of H-NS proteins by a phage protein.
Authors: Bdira, F.B. / Erkelens, A.M. / Qin, L. / Volkov, A.N. / Lippa, A.M. / Bowring, N. / Boyle, A.L. / Ubbink, M. / Dove, S.L. / Dame, R.T.
History
DepositionApr 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gp4


Theoretical massNumber of molelcules
Total (without water)5,6691
Polymers5,6691
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4130 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Gp4 / Gp4


Mass: 5668.792 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Gp4 / Source: (gene. exp.) Pseudomonas phage LUZ24 (virus) / Gene: gp4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A9J6U1

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D HN(COCA)CB
141isotropic13D HNCO
151isotropic13D HN(CA)CO
161isotropic13D HBHA(CO)NH
171isotropic13D (H)CCH-TOCSY
181isotropic13D (H)CCH-TOCSY
191isotropic12D 1H-13C HSQC
1101isotropic12D 1H-13C HSQC aromatic
1111isotropic13D 1H-15N NOESY
1121isotropic13D 1H-13C NOESY aliphatic
1131isotropic13D 1H-13C NOESY aromatic
1141isotropic12D (HB)CB(CGCD)HD
1151isotropic12D (HB)CB(CGCDCE)HE

-
Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] Gp4, 20 mM Bis-Tris, 150 mM potassium chloride, 1 mM EDTA, 5 % v/v [U-2H] D2O, 95% H2O/5% D2O
Label: sample1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMGp4[U-100% 13C; U-100% 15N]1
20 mMBis-Trisnatural abundance1
150 mMpotassium chloridenatural abundance1
1 mMEDTAnatural abundance1
5 % v/vD2O[U-2H]1
Sample conditionsIonic strength: 170 mM / Label: condition1 / pH: 6 / Pressure: 1 atm / Temperature: 293 K

-
NMR measurement

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

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNpeak picking
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLORBrungerrefinement
Refinement
MethodSoftware ordinal
simulated annealing8
torsion angle dynamics9
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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