[English] 日本語
Yorodumi
- PDB-2lt4: CdnLNt from Myxoccoccus xanthus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lt4
TitleCdnLNt from Myxoccoccus xanthus
ComponentsTranscriptional regulator, CarD family
KeywordsTRANSCRIPTION / CdnL / CarD / TRCF-RID / PF02559 / RNA polymerase
Function / homology
Function and homology information


: / : / CarD, C-terminal domain / 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 / Thrombin, subunit H - #170 / Thrombin, subunit H ...: / : / CarD, C-terminal domain / 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 / Thrombin, subunit H - #170 / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Transcriptional regulator, CarD family
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsJimenez, M.A. / Padmanabhan, S. / Mirassou, Y.
Citation
Journal: Plos One / Year: 2014
Title: Structural Insights into RNA Polymerase Recognition and Essential Function of Myxococcus xanthus CdnL.
Authors: Gallego-Garcia, A. / Mirassou, Y. / Garcia-Moreno, D. / Elias-Arnanz, M. / Jimenez, M.A. / Padmanabhan, S.
#1: Journal: To be Published
Title: 1H, 13C and 15N assignments of CdnL, an essential protein in Myxococcus xanthus
Authors: Mirassou, Y. / Elias-Arnanz, M. / Padmanabhan, S. / Jimenez, M.
History
DepositionMay 14, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: 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
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator, CarD family


Theoretical massNumber of molelcules
Total (without water)7,7861
Polymers7,7861
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 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Transcriptional regulator, CarD family


Mass: 7785.888 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Strain: DK 1622 / Gene: MXAN_2627 / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1D927

-
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 HN(CA)CB
11133D CBCA(CO)NH
11233D HBHA(CO)NH
11342D 1H-13C HSQC aliphatic
11443D (H)CCH-TOCSY
11543D 1H-13C NOESY aliphatic
11652D 1H-15N HSQC
11753D HNCA
11853D CBCA(CO)NH
11953D HBHA(CO)NH
22032D 1H-15N HSQC
22133D HNCO
22233D HNCA
22333D HN(CA)CB
22433D CBCA(CO)NH
22533D HBHA(CO)NH
12622D 1H-13C HSQC aromatic

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM CdnLNt, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 % sodium azide, 0.5 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21 mM CdnLNt, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 % sodium azide, 0.5 mM DSS, 100% D2O100% D2O
31 mM [U-100% 13C; U-100% 15N] CdnLNt, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 % sodium azide, 0.5 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-100% 13C; U-100% 15N] CdnLNt, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 % sodium azide, 0.5 mM DSS, 100% D2O100% D2O
50.5 mM [U-100% 13C; U-100% 15N] CdnLNt, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 % sodium azide, 0.25 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCdnLNt-11
50 mMsodium phosphate-21
100 mMsodium chloride-31
0.05 %sodium azide-41
0.5 mMDSS-51
1 mMCdnLNt-62
50 mMsodium phosphate-72
100 mMsodium chloride-82
0.05 %sodium azide-92
0.5 mMDSS-102
1 mMCdnLNt-11[U-100% 13C; U-100% 15N]3
50 mMsodium phosphate-123
100 mMsodium chloride-133
0.05 %sodium azide-143
0.5 mMDSS-153
1 mMCdnLNt-16[U-100% 13C; U-100% 15N]4
50 mMsodium phosphate-174
100 mMsodium chloride-184
0.05 %sodium azide-194
0.5 mMDSS-204
0.5 mMCdnLNt-21[U-100% 13C; U-100% 15N]5
50 mMsodium phosphate-225
100 mMsodium chloride-235
0.05 %sodium azide-245
0.25 mMDSS-255
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1571 atm298 K
20.1571 atm288 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
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 494 / NOE intraresidue total count: 211 / NOE long range total count: 148 / NOE medium range total count: 59 / NOE sequential total count: 76 / Protein phi angle constraints total count: 63 / Protein psi angle constraints total count: 48
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://pdbjlc1.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