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- PDB-2lj6: Solution Structure and DNA-binding Properties of the Phosphoester... -

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Basic information

Entry
Database: PDB / ID: 2lj6
TitleSolution Structure and DNA-binding Properties of the Phosphoesterase Domain of DNA Ligase D
ComponentsProbable ATP-dependent DNA ligase
KeywordsDNA BINDING PROTEIN / PHOSPHOESTERASE
Function / homology
Function and homology information


RNA exonuclease activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA biosynthetic process / nucleotidyltransferase activity / DNA recombination / DNA-directed DNA polymerase activity / DNA repair / DNA binding / ATP binding / metal ion binding
Similarity search - Function
DNA ligase D / LigD polymerase domain, PaeLigD-type / DNA ligase D, ligase domain / LigD, primase-polymerase domain / DNA ligase D, polymerase domain / DNA ligase D, 3'-phosphoesterase domain / DNA polymerase Ligase (LigD) / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / ATP-dependent DNA ligase family profile. ...DNA ligase D / LigD polymerase domain, PaeLigD-type / DNA ligase D, ligase domain / LigD, primase-polymerase domain / DNA ligase D, polymerase domain / DNA ligase D, 3'-phosphoesterase domain / DNA polymerase Ligase (LigD) / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Multifunctional non-homologous end joining protein LigD
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 3
AuthorsDutta, K. / Natarajan, A. / Shuman, S. / Ghose, R.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Solution structure and DNA-binding properties of the phosphoesterase domain of DNA ligase D.
Authors: Natarajan, A. / Dutta, K. / Temel, D.B. / Nair, P.A. / Shuman, S. / Ghose, R.
History
DepositionSep 6, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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_spectrometer.model
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: Probable ATP-dependent DNA ligase


Theoretical massNumber of molelcules
Total (without water)20,2581
Polymers20,2581
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)15 / 2048structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Probable ATP-dependent DNA ligase


Mass: 20257.938 Da / Num. of mol.: 1 / Fragment: UNP residues 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA2138 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I1X7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-15N HSQC
1433D HN(CA)CB
1533D HNCO
1633D HNCA
1733D TROSY
1833D HN(COCA)CB
1933D HN(CO)CA
11033D HN(CA)CO
11123D CC(CO)NH
11223D H(CCO)NH
11323D HBHA(CO)NH
11423D 1H-15N NOESY
11523D 1H-13C NOESY aliphatic
11623D 1H-13C NOESY aromatic
NMR detailsText: All Backbone experiments were TROSY based

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Sample preparation

Details
Solution-IDContentsSolvent system
1300 uM [U-100% 15N] Pae177, 10 % D20, 90 % H20, 50 mM Bis-Tris, 200 mM NaCl, 5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
2300 uM [U-100% 13C; U-100% 15N] Pae177, 10 % D20, 90 % H20, 50 mM Bis-Tris, 200 mM NaCl, 5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
3300 uM [U-13C; U-15N; U-2H] Pae177, 10 % D20, 90 % H20, 50 mM Bis-Tris, 200 mM NaCl, 5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMPae177-1[U-100% 15N]1
10 %D20-21
90 %H20-31
50 mMBis-Tris-41
200 mMNaCl-51
5 mMDTT-61
300 uMPae177-7[U-100% 13C; U-100% 15N]2
10 %D20-82
90 %H20-92
50 mMBis-Tris-102
200 mMNaCl-112
5 mMDTT-122
300 uMPae177-13[U-13C; U-15N; U-2H]3
10 %D20-143
90 %H20-153
50 mMBis-Tris-163
200 mMNaCl-173
5 mMDTT-183
Sample conditionsIonic strength: 200 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
NMRView8.1.27Johnson, One Moon Scientificchemical shift assignment
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2080 / NOE intraresidue total count: 488 / NOE long range total count: 419 / NOE medium range total count: 53 / NOE sequential total count: 153
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 2048 / Conformers submitted total number: 15 / Maximum upper distance constraint violation: 5 Å

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