[English] 日本語
Yorodumi
- PDB-2l3u: Solution Structure of Domain IV from the YbbR family protein of D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l3u
TitleSolution Structure of Domain IV from the YbbR family protein of Desulfitobacterium hafniense: Northeast Structural Genomics Consortium target DhR29A
ComponentsYbbR family protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta strand / figure eight / figure 8 / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyRNA Polymerase Alpha Subunit; Chain A, domain 2 - #30 / YbbR-like / YbbR-like protein / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Beta Complex / Mainly Beta / YbbR family protein
Function and homology information
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsBarb, A.W. / Lee, H. / Belote, R.L. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Prestegard, J.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Protein Sci. / Year: 2011
Title: Structures of domains I and IV from YbbR are representative of a widely distributed protein family.
Authors: Barb, A.W. / Cort, J.R. / Seetharaman, J. / Lew, S. / Lee, H.W. / Acton, T. / Xiao, R. / Kennedy, M.A. / Tong, L. / Montelione, G.T. / Prestegard, J.H.
History
DepositionSep 23, 2010Deposition site: BMRB / Processing site: RCSB
SupersessionOct 6, 2010ID: 2KPS
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
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: YbbR family protein


Theoretical massNumber of molelcules
Total (without water)11,2691
Polymers11,2691
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)10 / 200back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1fewest violations

-
Components

#1: Protein YbbR family protein


Mass: 11269.006 Da / Num. of mol.: 1 / Fragment: sequence database residues 321-409
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: DCB-2 / DSM 10664 / Gene: Dhaf_0833 / Production host: Escherichia coli (E. coli) / References: UniProt: B8FX10

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D HN(CO)CA
1413D H(CCO)NH
1513D (H)CCH-TOCSY
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D HNCO
1922D 1H-15N HSQC
11023D HNCO
11132D 1H-15N HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] DhR29a, 200 mM sodium chloride, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C] DhR29a, 10 % D2O, 200 mM sodium chloride, 1 mg Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
31 mM DhR29a, 200 mM sodium chloride, 10 % D2O, 7 % acrylamide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDhR29a-1[U-100% 13C; U-100% 15N]1
200 mMsodium chloride-21
10 %D2O-31
1 mMDhR29a-4[U-13C]2
10 %D2O-52
200 mMsodium chloride-62
1 mg/mLPf1 phage-72
1 mMDhR29a-83
200 mMsodium chloride-93
10 %D2O-103
7 %acrylamide-113
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: refinement completed using XPLOR-NIH and 3 RDC datasets, NOE list, and dihedral angle constraints
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 200 / 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://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