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- PDB-2ltd: Solution NMR Structure of apo YdbC from Lactococcus lactis, North... -

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Basic information

Entry
Database: PDB / ID: 2ltd
TitleSolution NMR Structure of apo YdbC from Lactococcus lactis, Northeast Structural Genomics Consortium (NESG) Target KR150
ComponentsUncharacterized protein ydbC
KeywordsStructural Genomics / Unknown Function / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
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
Transcriptional coactivator p15 (PC4) C-terminal domain-containing protein
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis Il1403 (lactic acid bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsRossi, P. / Barbieri, C.M. / Aramini, J.M. / Bini, E. / Lee, H. / Janjua, H. / Ciccosanti, C. / Wang, H. / Acton, T.B. / Xiao, R. ...Rossi, P. / Barbieri, C.M. / Aramini, J.M. / 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 16, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 6, 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

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Assembly

Deposited unit
A: Uncharacterized protein ydbC
B: Uncharacterized protein ydbC


Theoretical massNumber of molelcules
Total (without water)18,9782
Polymers18,9782
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 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 Il1403 (lactic acid bacteria)
Strain: IL1403 / Gene: L114363, LL0313, ydbC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q9CIP3

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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 CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
1713D 1H-13C NOESY aliphatic
1813D 1H-13C NOESY aromatic
1913D 1H-15N NOESY
11033D-X-filt-13C-editedNOESY
11113D (H)CCH-TOCSY
11213D HBHA(CO)NH
11313D HN(CA)CO
11413D (H)CCH-COSY
11513D CCH-TOCSY
11621H-15N Hetnoe
11711D T1
11811D T2(CPMG)
1192j-mod HSQC (rdc)

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 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, 90% H2O/10% D2O90% H2O/10% D2O
20.697 mM [U-5% 13C; U-100% 15N] KR150.020, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl, 90% H2O/10% D2O90% H2O/10% D2O
31.2 mM KR150.019, 0.02 % NaN3, 10 mM DTT, 100 mM NaCL, 10 % D2O, 50 uM DSS, 10 mM TRIS-HCl, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 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
0.697 mMKR150.020-8[U-5% 13C; U-100% 15N]2
0.02 %NaN3-92
10 mMDTT-102
100 mMNaCL-112
10 %D2O-122
50 uMDSS-132
10 mMTRIS-HCl-142
1.2 mMKR150.019-153
0.02 %NaN3-163
10 mMDTT-173
100 mMNaCL-183
10 %D2O-193
50 uMDSS-203
10 mMTRIS-HCl-213
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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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
PALESPALES (Zweckstetter, Bax)geometry optimization
PSVSBhattacharya, Montelionestructure validation
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: RESTRAINED MD IN WATER BATH, PARAM19, NCS SYMMETRY
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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