[English] 日本語
Yorodumi
- PDB-1rwu: Solution structure of conserved protein YbeD from E. coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rwu
TitleSolution structure of conserved protein YbeD from E. coli
ComponentsHypothetical UPF0250 protein ybeD
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / mixed alpha-beta fold / Protein Structure Initiative / PSI / Northeast Structural Genomics Consortium / NESG
Function / homologyUncharacterised protein family UPF0250, YbeD-like / YbeD-like domain superfamily / Protein of unknown function (DUF493) / ACT domain / Alpha-Beta Plaits / 2-Layer Sandwich / cytosol / Alpha Beta / UPF0250 protein YbeD
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsKozlov, G. / Arrowsmith, C.H. / Gehring, K. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Bacteriol. / Year: 2004
Title: Structural similarity of YbeD protein from Escherichia coli to allosteric regulatory domains
Authors: Kozlov, G. / Elias, D. / Semesi, A. / Yee, A. / Cygler, M. / Gehring, K.
History
DepositionDec 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical UPF0250 protein ybeD


Theoretical massNumber of molelcules
Total (without water)12,4221
Polymers12,4221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1fewest violations

-
Components

#1: Protein Hypothetical UPF0250 protein ybeD


Mass: 12422.073 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YBED, B0631, C0721, Z0776, ECS0669, SF0650, S0672 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A8J4

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
1322D NOESY
1432D NOESY
NMR detailsText: This structure was determined using standard triple-resonance and homonuclear techniques.

-
Sample preparation

Details
Solution-IDContentsSolvent system
12mM YbeD U-15N; 50mM phosphate buffer; 300mM NaCl; 0.1mM sodium azide90% H2O/10% D2O
22mM YbeD; 50mM phosphate buffer; 300mM NaCl; 0.1mM sodium azide90% H2O/10% D2O
32mM YbeD; 50mM phosphate buffer; 300mM NaCl; 0.1mM sodium azide100% D2O
Sample conditionsIonic strength: 300mM NaCl / pH: 6.3 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Bruker Biospincollection
XwinNMR2.1Bruker Biospinprocessing
Gifa4.31Delsucprocessing
XEASY1.3.13Wuthrichdata analysis
CYANA1.0.6Guentertstructure solution
Xplor-NIH2.9.2Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 556 restraints, 393 are NOE-derived distance constraints, 131 TALOS-derived dihedral angle restraints, 32 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

+
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