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- PDB-2lt1: Solution NMR structure of the 72-residue N-terminal domain of Myx... -

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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


rRNA transcription / DNA binding
Similarity search - Function
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 / DNA binding domain with preference for A/T rich regions / Thrombin, subunit H - #170 ...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 / 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
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: CarD protein


Theoretical massNumber of molelcules
Total (without water)7,8891
Polymers7,8891
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 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

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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
11543D (H)CCH-TOCSY
11643D 1H-13C NOESY

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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 / Pressure: ambient / Temperature: 298 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
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

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