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- PDB-2lt4: CdnLNt from Myxoccoccus xanthus -

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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-like, C-terminal domain / : / : / CarD, 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-like, C-terminal domain / : / : / CarD, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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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

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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

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NMR measurement

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

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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

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