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- PDB-1tn9: THE SOLUTION STRUCTURE OF TN916 INTEGRASE N-TERMINAL DOMAIN/DNA C... -

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Basic information

Entry
Database: PDB / ID: 1tn9
TitleTHE SOLUTION STRUCTURE OF TN916 INTEGRASE N-TERMINAL DOMAIN/DNA COMPLEX
Components
  • DNA (5'-D(*GP*AP*AP*TP*TP*TP*AP*CP*TP*AP*CP*TP*C)-3')
  • DNA (5'-D(*GP*AP*GP*TP*AP*GP*TP*AP*AP*AP*TP*TP*C)-3')
  • PROTEIN (INTEGRASE)
KeywordsINTEGRASE/DNA / INTEGRASE / DNA BINDING / TRANSPOSITION / COMPLEX / BETA-SHEET RECOGNITION / INTEGRASE-DNA COMPLEX
Function / homology
Function and homology information


integrase activity / viral genome integration into host DNA / establishment of integrated proviral latency / DNA recombination / symbiont entry into host cell / DNA binding
Similarity search - Function
Integrase, Tn916-type, N-terminal DNA binding / DNA binding domain of tn916 integrase / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Phage integrase family / Integrase, catalytic domain / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core ...Integrase, Tn916-type, N-terminal DNA binding / DNA binding domain of tn916 integrase / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Phage integrase family / Integrase, catalytic domain / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core / Classic Zinc Finger / DNA-binding domain superfamily / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Transposase from transposon Tn916
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
synthetic construct (others)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsClubb, R.T. / Wojciak, J.M. / Connolly, K.M.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: NMR structure of the Tn916 integrase-DNA complex.
Authors: Wojciak, J.M. / Connolly, K.M. / Clubb, R.T.
History
DepositionJan 21, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 2.0Oct 16, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy
Category: atom_site / ndb_struct_na_base_pair_step ...atom_site / ndb_struct_na_base_pair_step / pdbx_entity_src_syn / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _pdbx_nmr_software.authors / _pdbx_nmr_software.version / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 2.1Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*GP*AP*GP*TP*AP*GP*TP*AP*AP*AP*TP*TP*C)-3')
C: DNA (5'-D(*GP*AP*AP*TP*TP*TP*AP*CP*TP*AP*CP*TP*C)-3')
A: PROTEIN (INTEGRASE)


Theoretical massNumber of molelcules
Total (without water)16,1183
Polymers16,1183
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3340 Å2
ΔGint-26 kcal/mol
Surface area8490 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LEAST RESTRAINT VIOLATION
Representative

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Components

#1: DNA chain DNA (5'-D(*GP*AP*GP*TP*AP*GP*TP*AP*AP*AP*TP*TP*C)-3')


Mass: 4014.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*AP*AP*TP*TP*TP*AP*CP*TP*AP*CP*TP*C)-3')


Mass: 3925.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein PROTEIN (INTEGRASE)


Mass: 8177.321 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DNA BINDING DOMAIN / Mutation: C57A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: BL21(DE3) / Cellular location: CYTOPLASM / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22886

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY ETC.
NMR detailsText: THREE AND FOUR-DIMENSIONAL HETERONUCLEAR NMR EXPERIMENTS

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Sample preparation

Sample conditionspH: 6.0 / Temperature: 305 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.843BRUNGERrefinement
XPLOR3.843BRUNGERstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 20

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