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- PDB-2ltt: Solution NMR Structure of YdbC:dT19G1 complex. Northeast Structur... -

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Basic information

Entry
Database: PDB / ID: 2ltt
TitleSolution NMR Structure of YdbC:dT19G1 complex. Northeast Structural Genomics Consortium (NESG) Target KR150
Components
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Putative uncharacterized protein ydbC
KeywordsTRANSCRIPTION / DNA BINDING PROTEIN/DNA / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcriptional Co-activator pc4; Chain A - #70 / PC4-like / Transcriptional coactivator p15 (PC4), C-terminal / Transcriptional Coactivator p15 (PC4) / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional coactivator p15 (PC4) C-terminal domain-containing protein
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodSOLUTION NMR / restrained molecular dynamics
Model detailslowest energy, model 1
AuthorsRossi, P. / Barbieri, C.M. / Aramini, J.A. / Bini, E. / Lee, H. / Janjua, H. / Ciccosanti, C. / Wang, H. / Acton, T.B. / Xiao, R. ...Rossi, P. / Barbieri, C.M. / Aramini, J.A. / Bini, E. / Lee, H. / Janjua, H. / Ciccosanti, C. / Wang, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome.
Authors: Rossi, P. / Barbieri, C.M. / Aramini, J.M. / Bini, E. / Lee, H.W. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T.
History
DepositionMay 31, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3Mar 6, 2013Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein ydbC
B: Putative uncharacterized protein ydbC
C: DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)24,1043
Polymers24,1043
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative uncharacterized protein ydbC


Mass: 9488.755 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Strain: IL1403 / Gene: ydbC, LL0313, L114363 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CIP3
#2: DNA chain DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 5126.320 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D 1H-13C NOESY aliphatic
1613D 1H-13C NOESY aromatic
1713D 1H-15N NOESY
1813D-13C,15N X-filt-13C,15N-editedNOESY
1913D HN(CA)CO
11011H-15N Hetnoe
11111D T1
11211D T2(CPMG)
11312D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.6 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl, 0.3 mM DNA (5'- ...Contents: 0.6 mM [U-100% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl, 0.3 mM DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*G)-3'), 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMKR150.020-1[U-100% 13C; U-100% 15N]1
0.02 %NaN3-21
10 mMDTT-31
100 mMNaCL-41
10 %D2O-51
50 uMDSS-61
10 mMTRIS-HCl-71
0.3 mMDNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*G)-3')-81
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
VnmrJVariancollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESZweckstetter, Baxgeometry optimization
PSVSBhattacharya, Montelionestructure validation
HADDOCKBonvin A. M. J. J.refinement
HADDOCKBonvin A. M. J. J.structure solution
HADDOCKBonvin A. M. J. J.geometry optimization
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
Details: RESTRAINED MD IN WATER BATH, OPLSX, NCS SYMMETRY, C2 SYMMETRY WITHIN HADDOCK INTERFACE
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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