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- PDB-2lt3: Solution NMR structure of the C-terminal domain of CdnL from Myxo... -

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Basic information

Entry
Database: PDB / ID: 2lt3
TitleSolution NMR structure of the C-terminal domain of CdnL from Myxococcus xanthus
ComponentsTranscriptional regulator, CarD familyTranscriptional regulation
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, 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator, CarD family
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsMirassou, Y. / Garcia-Moreno, D. / Padmanabhan, S. / Jimenez, M.A.
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: Biomol.Nmr Assign. / Year: 2009
Title: 1H, 13C and 15N backbone and side chain resonance assignments of the C-terminal domain of CdnL from Myxococcus xanthus.
Authors: Mirassou, Y. / Garcia-Moreno, D. / Santiveri, C.M. / Santoro, J. / Elias-Arnanz, M. / Padmanabhan, S. / Jimenez, M.A.
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)13,0431
Polymers13,0431
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

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Components

#1: Protein Transcriptional regulator, CarD family / Transcriptional regulation


Mass: 13042.906 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Strain: DK 1622 / Gene: MXAN_2627 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCA
1513D HN(CO)CA
1613D HNCO
1713D HBHANH
1813D HBHA(CO)NH
1913D HA(CA)NH
11012D 1H-13C HSQC
11113D 1H-15N NOESY
11223D (H)CCH-TOCSY
11323D (H)CCH-TOCSY
11423D 1H-13C NOESY
11532D 1H-1H COSY
11632D 1H-1H TOCSY
11732D 1H-1H NOESY
11842D 1H-1H COSY
11942D 1H-1H TOCSY
12042D 1H-1H NOESY
12142D 1H-13C HSQC
12213D 1H-15N NOESY
12332D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM [U-100% 13C; U-100% 15N] CdnLCt, 100 mM sodium chloride, 50 mM sodium phosphate, 2 mM beta-mercaptoethanol, 0.05 % sodium azide, 0.2 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
22 mM [U-100% 13C; U-100% 15N] CdnLCt, 100 mM sodium chloride, 50 mM sodium phosphate, 2 mM beta-mercaptoethanol, 0.05 % sodium azide, 0.2 mM DSS, 100% D2O100% D2O
31.5 mM CdnLCt, 100 mM sodium chloride, 50 mM sodium phosphate, 2 mM beta-mercaptoethanol, 0.05 % sodium azide, 0.2 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
41.5 mM CdnLCt, 100 mM sodium chloride, 50 mM sodium phosphate, 2 mM beta-mercaptoethanol, 0.05 % sodium azide, 0.2 mM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMCdnLCt-1[U-100% 13C; U-100% 15N]1-21
100 mMsodium chloride-21
50 mMsodium phosphate-31
2 mMbeta-mercaptoethanol-41
0.05 %sodium azide-51
0.2 mMDSS-61
2 mMCdnLCt-7[U-100% 13C; U-100% 15N]2
100 mMsodium chloride-82
50 mMsodium phosphate-92
2 mMbeta-mercaptoethanol-102
0.05 %sodium azide-112
0.2 mMDSS-122
1.5 mMCdnLCt-133
100 mMsodium chloride-143
50 mMsodium phosphate-153
2 mMbeta-mercaptoethanol-163
0.05 %sodium azide-173
0.2 mMDSS-183
1.5 mMCdnLCt-194
100 mMsodium chloride-204
50 mMsodium phosphate-214
2 mMbeta-mercaptoethanol-224
0.05 %sodium azide-234
0.2 mMDSS-244
Sample conditionsIonic strength: 150 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxdihedral angle constraints
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: 2088 / NOE intraresidue total count: 570 / NOE long range total count: 644 / NOE medium range total count: 543 / NOE sequential total count: 331 / Protein phi angle constraints total count: 106 / Protein psi angle constraints total count: 87
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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