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- PDB-2coe: Solution structure of BRCT domain of terminal deoxynucleotidyltra... -

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Basic information

Entry
Database: PDB / ID: 2coe
TitleSolution structure of BRCT domain of terminal deoxynucleotidyltransferase
Componentsdeoxynucleotidyltransferase, terminal variant
KeywordsTRANSFERASE / BRCT domain / DNA polymerase / teminal deoxynucleotidyltransferase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / DNA modification / DNA metabolic process / response to ATP / euchromatin / nuclear matrix / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase activity / DNA binding ...DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / DNA modification / DNA metabolic process / response to ATP / euchromatin / nuclear matrix / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
DNA nucleotidylexotransferase (TdT) / BRCT domain / Polymerase, nucleotidyl transferase domain / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Nucleotidyltransferase domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X ...DNA nucleotidylexotransferase (TdT) / BRCT domain / Polymerase, nucleotidyl transferase domain / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Nucleotidyltransferase domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA nucleotidylexotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNagashima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of BRCT domain of terminal deoxynucleotidyltransferase
Authors: Nagashima, T. / Hayashi, F. / Yokoyama, S.
History
DepositionMay 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 / 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 / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: deoxynucleotidyltransferase, terminal variant


Theoretical massNumber of molelcules
Total (without water)12,9011
Polymers12,9011
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,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein deoxynucleotidyltransferase, terminal variant


Mass: 12900.611 Da / Num. of mol.: 1 / Fragment: BRCA1 C-turminus (BRCT) domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: DNTT, TDT / Plasmid: P040621-11 / References: UniProt: P04053, DNA nucleotidylexotransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.26mM BRCT doamin U-13C,15N; 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.901Kobayashi, N.data analysis
CYANA1.07Guntert, P.structure solution
CYANA1.07Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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