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- PDB-2lqk: NMR solution structure of the N-terminal domain of the CdnL prote... -

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Basic information

Entry
Database: PDB / ID: 2lqk
TitleNMR solution structure of the N-terminal domain of the CdnL protein from Thermus thermophilus
ComponentsTranscriptional regulatorTranscriptional regulation
KeywordsTranscription regulator / RNA polymerase interacting domain
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 / Thrombin, subunit H - #170 / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Transcriptional regulator
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model 1
AuthorsJimenez, M. / Padmanabhan, S.
CitationJournal: J.Biomol.Nmr / Year: 2012
Title: NMR structure note: N-terminal domain of Thermus thermophilus CdnL.
Authors: Gallego-Garcia, A. / Mirassou, Y. / Elias-Arnanz, M. / Padmanabhan, S. / Jimenez, M.A.
History
DepositionMar 9, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: 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


Theoretical massNumber of molelcules
Total (without water)7,4481
Polymers7,4481
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 / Transcriptional regulation


Mass: 7448.497 Da / Num. of mol.: 1 / Fragment: UNP residues 1-67
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: cdnL, TT_C1818 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72GN0

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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 CBCA(CO)NH
11133D HN(CA)CB
11233D HBHA(CO)NH
11333D HBHANH
11442D 1H-13C HSQC aliphatic
11542D 1H-13C HSQC aromatic
11643D (H)CCH-TOCSY
11743D 1H-13C NOESY
21832D 1H-15N HSQC
31932D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM TtCdnLNt, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 % sodium azide, 0.5 mM DSS, 90 % H2O, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
21 mM TtCdnLNt, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 % sodium azide, 0.5 mM DSS, 100 % D2O, 100% D2O100% D2O
31 mM [U-100% 13C; U-100% 15N] TtCdnLNt, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 % sodium azide, 0.5 mM DSS, 90 % H2O, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-100% 13C; U-100% 15N] TtCdnLNt, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 % sodium azide, 0.5 mM DSS, 100 % D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTtCdnLNt-11
50 mMsodium phosphate-21
100 mMsodium chloride-31
0.05 %sodium azide-41
0.5 mMDSS-51
90 %H2O-61
10 %D2O-71
1 mMTtCdnLNt-82
50 mMsodium phosphate-92
100 mMsodium chloride-102
0.05 %sodium azide-112
0.5 mMDSS-122
100 %D2O-132
1 mMTtCdnLNt-14[U-100% 13C; U-100% 15N]3
50 mMsodium phosphate-153
100 mMsodium chloride-163
0.05 %sodium azide-173
0.5 mMDSS-183
90 %H2O-193
10 %D2O-203
1 mMTtCdnLNt-21[U-100% 13C; U-100% 15N]4
50 mMsodium phosphate-224
100 mMsodium chloride-234
0.05 %sodium azide-244
0.5 mMDSS-254
100 %D2O-264
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.15 7.0 ambient 298 K
20.15 7.0 ambient 288 K
30.15 7.0 ambient 308 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
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 981 / NOE intraresidue total count: 217 / NOE long range total count: 461 / NOE medium range total count: 96 / NOE sequential total count: 207 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 64 / Protein psi angle constraints total count: 45
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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