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- PDB-1l7b: Solution NMR Structure of BRCT Domain of T. Thermophilus: Northea... -

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Basic information

Entry
Database: PDB / ID: 1l7b
TitleSolution NMR Structure of BRCT Domain of T. Thermophilus: Northeast Structural Genomics Consortium Target WR64TT
ComponentsDNA LIGASE
KeywordsLIGASE / BRCT / DNA LIGASE / AUTOSTRUCTURE / STRUCTURAL GENOMICS / NESG / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


DNA ligase (NAD+) / DNA ligase (NAD+) activity / DNA replication / DNA repair / DNA binding / metal ion binding
Similarity search - Function
NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation / NAD-dependent DNA ligase, N-terminal / NAD-dependent DNA ligase adenylation domain / NAD-dependent DNA ligase OB-fold domain ...NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation / NAD-dependent DNA ligase, N-terminal / NAD-dependent DNA ligase adenylation domain / NAD-dependent DNA ligase OB-fold domain / Ligase N family / DisA/LigA, helix-hairpin-helix motif / Helix-hairpin-helix motif / BRCT domain / RuvA domain 2-like / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding, OB-fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsSahota, G. / Dixon, B.L. / Huang, Y.P. / Aramini, J. / Monleon, D. / Bhattacharya, D. / Swapna, G.V.T. / Yin, C. / Xiao, R. / Anderson, S. ...Sahota, G. / Dixon, B.L. / Huang, Y.P. / Aramini, J. / Monleon, D. / Bhattacharya, D. / Swapna, G.V.T. / Yin, C. / Xiao, R. / Anderson, S. / Tejero, R. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of the Brct Domain from Thermus Thermophilus DNA Ligase
Authors: Sahota, G. / Dixon, B.L. / Huang, Y.P. / Aramini, J. / Bhattacharya, A. / Monleon, D. / Swapna, G.V.T. / Yin, C. / Xiao, R. / Anderson, S. / Montelione, G.T. / Tejero, R.
History
DepositionMar 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA LIGASE


Theoretical massNumber of molelcules
Total (without water)10,0311
Polymers10,0311
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)10 / 100set of all structures within 5RT of LOWEST ENERGY STRUCTURE
RepresentativeModel #1

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Components

#1: Protein DNA LIGASE /


Mass: 10030.583 Da / Num. of mol.: 1 / Fragment: BRCT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: DNLJ / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P26996, DNA ligase (NAD+)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D PFG-[15N]HSQC
1213D PFG- 3D PFG-(HA)CA(CO)NH
1313D PFG-HA(CA)(CO)NH
1413D PFG-HA(CA)NH
1513D PFG-CBCANH
1613D PFG-CBCA(CO)NH
1713D PFG-(HA)CANH
1813D PFG-H 3D PFG-HBHA(CB)(CA)(CO)NH
1913D PFG-HCC(CO)NH-TOCSY
11013D PFG-13C-EDITED NOESY
11113D PFG-15N-EDITED NOESY
11212D HSQC-J
1131N-H IPAP RESIDUAL DIPOLAR COUPLING MEASUREMENTS
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.3mM U-15N,13C; 300mM NH4OAc; 95% H20, 10% D20 / Solvent system: 95% H20, 10% D20
Sample conditionsIonic strength: 300mM NH4OAc / pH: 6.2 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVARIANcollection
VNMR6.1BVARIANprocessing
NMRPipe97.231.15.18Delaglioprocessing
AutoAssign1.7.6Moseleydata analysis
AutoStructure1.0 BetaHuangdata analysis
DYANA1.5Guntertstructure solution
DYANA1.5Guntert, Wuthrich, et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: X-PLOR-NIH VERSION 1.1.2 (G.M. CLORE,J. KUSZEWSKY,C. SCHWIETERS,N. TJANDRA) was also used for refinement
NMR ensembleConformer selection criteria: set of all structures within 5RT of LOWEST ENERGY STRUCTURE
Conformers calculated total number: 100 / Conformers submitted total number: 10

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