[English] 日本語
Yorodumi
- PDB-2jrx: Solution NMR structure of protein YejL from E. coli. Northeast St... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jrx
TitleSolution NMR structure of protein YejL from E. coli. Northeast Structural Genomics target ER309
ComponentsUPF0352 protein yejL
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / homodimer / alpha helix / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyUncharacterised protein family UPF0352 / YejL-like superfamily / Protein of unknown function (DUF1414) / YejL-like / YejL-like / Orthogonal Bundle / Mainly Alpha / cytosol / UPF0352 protein YejL
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailsstructure of YejL homodimer
AuthorsCort, J.R. / Zhao, L. / Jiang, M. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. ...Cort, J.R. / Zhao, L. / Jiang, M. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Chemical Shift Assignments of E. coli YejL protein.
Authors: Cort, J.R. / Montelione, G.T. / Acton, T.B. / Kennedy, M.A.
History
DepositionJun 29, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UPF0352 protein yejL
B: UPF0352 protein yejL


Theoretical massNumber of molelcules
Total (without water)18,7352
Polymers18,7352
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)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

-
Components

#1: Protein UPF0352 protein yejL


Mass: 9367.579 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein is a homodimer in solution / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yejL, b2187, JW2175 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P0AD24

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR / Details: structure of YejL homodimer
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D HNHA
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11224d 1H-13C-13C-1H HMQC NOESY
11313D 1H-13C edited-filtered NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-100% 13C; U-100% 15N] protein, 5 % D2O, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % sodium azide, 5 mM calcium chloride, 95% H2O/5% D2O95% H2O/5% D2O
21.5 mM [U-100% 13C; U-100% 15N] protein, 100 % D2O, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % sodium azide, 5 mM calcium chloride, 100% D2O100% D2O
31.5 mM [5% biosynthetically directed 13C labeling; U-100% 15N] protein, 5 % D2O, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % sodium azide, 5 mM calcium chloride, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMYejL[U-100% 13C; U-100% 15N]1
5 %D2O1
100 mMsodium chloride1
20 mMammonium acetate1
10 mMDTT1
0.02 %sodium azide1
5 mMcalcium chloride1
1.5 mMYejL[U-100% 13C; U-100% 15N]2
100 %D2O2
100 mMsodium chloride2
20 mMammonium acetate2
10 mMDTT2
0.02 %sodium azide2
5 mMcalcium chloride2
1.5 mMYejL[5% biosynthetically directed 13C labeling; U-100% 15N]3
5 %D2O3
100 mMsodium chloride3
20 mMammonium acetate3
10 mMDTT3
0.02 %sodium azide3
5 mMcalcium chloride3
Sample conditionsIonic strength: 130 / pH: 5.5 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

-
Processing

NMR software
NameVersionDeveloperClassification
VNMRVariancollection
Felix97Accelrys Software Inc.processing
SparkyGoddarddata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / 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://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