[English] 日本語
Yorodumi
- PDB-2lt1: Solution NMR structure of the 72-residue N-terminal domain of Myx... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lt1
TitleSolution NMR structure of the 72-residue N-terminal domain of Myxococcus xanthus CarD
ComponentsCarD protein
KeywordsTRANSCRIPTION / CarD / CdnL / TRCF-RID / PF02559
Function / homology
Function and homology information


CarD-like, C-terminal domain / CarD-like/TRCF, RNAP-interacting domain / CarD-like/TRCF, RNAP-interacting domain superfamily / CarD-like/TRCF RID domain / CarD-like/TRCF domain / DNA binding domain with preference for A/T rich regions / Thrombin, subunit H - #170 / AT hook, DNA-binding motif / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesMyxococcus xanthus (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsJimenez, M.A. / Padmanabhan, S.
CitationJournal: Plos One
Title: Structure-Function Dissection of Myxococcus xanthus CarD N-Terminal Domain, a Defining Member of the CarD_CdnL_TRCF Family of RNA Polymerase Interacting Proteins.
Authors: Bernal-Bernal, D. / Gallego-Garcia, A. / Garcia-Martinez, G. / Garcia-Heras, F. / Jimenez, M.A. / Padmanabhan, S. / Elias-Arnanz, M.
History
DepositionMay 10, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CarD protein


Theoretical massNumber of molelcules
Total (without water)7,8891
Polymers7,8891
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein CarD protein


Mass: 7889.117 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: carD / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q50887

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1422D 1H-1H COSY
1522D 1H-1H TOCSY
1622D 1H-1H NOESY
1732D 1H-15N HSQC
1833D HNCO
1933D HNCA
11033D CBCA(CO)NH
11133D HN(CA)CB
11233D HBHA(CO)NH
11333D HBHANH
11442D 1H-13C HSQC aliphatic
11543D (H)CCH-TOCSY
11643D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM CarD1, 50 mM sodium phosphate, 100 mM sodium chloride, 0.01 % sodium azide, 2 mM beta-mercaptoethanol, 0.5 mM DSS, 90 % H2O, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
21 mM CarD1, 50 mM sodium phosphate, 100 mM sodium chloride, 0.01 % sodium azide, 2 mM beta-mercaptoethanol, 0.5 mM DSS, 100 % D2O, 100% D2O100% D2O
31 mM [U-100% 13C; U-100% 15N] CarD1, 50 mM sodium phosphate, 100 mM sodium chloride, 0.01 % sodium azide, 2 mM beta-mercaptoethanol, 0.5 mM DSS, 90 % H2O, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-100% 13C; U-100% 15N] CarD1, 50 mM sodium phosphate, 100 mM sodium chloride, 0.01 % sodium azide, 2 mM beta-mercaptoethanol, 0.5 mM DSS, 100 % D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCarD1-72-11
50 mMsodium phosphate-21
100 mMsodium chloride-31
0.01 %sodium azide-41
2 mMbeta-mercaptoethanol-51
0.5 mMDSS-61
90 %H2O-71
10 %D2O-81
1 mMCarD1-72-92
50 mMsodium phosphate-102
100 mMsodium chloride-112
0.01 %sodium azide-122
2 mMbeta-mercaptoethanol-132
0.5 mMDSS-142
100 %D2O-152
1 mMCarD1-72-16[U-100% 13C; U-100% 15N]3
50 mMsodium phosphate-173
100 mMsodium chloride-183
0.01 %sodium azide-193
2 mMbeta-mercaptoethanol-203
0.5 mMDSS-213
90 %H2O-223
10 %D2O-233
1 mMCarD1-72-24[U-100% 13C; U-100% 15N]4
50 mMsodium phosphate-254
100 mMsodium chloride-264
0.01 %sodium azide-274
2 mMbeta-mercaptoethanol-284
0.5 mMDSS-294
100 %D2O-304
Sample conditionsIonic strength: 0.15 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
Amberrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 699 / NOE intraresidue total count: 223 / NOE long range total count: 219 / NOE medium range total count: 84 / NOE sequential total count: 173 / Protein other angle constraints total count: 121 / Protein phi angle constraints total count: 67 / Protein psi angle constraints total count: 54
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / 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