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- PDB-1bb8: N-TERMINAL DNA BINDING DOMAIN FROM TN916 INTEGRASE, NMR, 25 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1bb8
TitleN-TERMINAL DNA BINDING DOMAIN FROM TN916 INTEGRASE, NMR, 25 STRUCTURES
ComponentsINTEGRASE
KeywordsINTEGRASE / DNA BINDING / TRANSPOSITION
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
Transposase from transposon Tn916
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsClubb, R.T. / Connolly, K.M. / Wojciak, J.M.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Site-specific DNA binding using a variation of the double stranded RNA binding motif.
Authors: Connolly, K.M. / Wojciak, J.M. / Clubb, R.T.
History
DepositionApr 29, 1998Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTEGRASE


Theoretical massNumber of molelcules
Total (without water)8,4631
Polymers8,4631
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)25 / 100LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein INTEGRASE /


Mass: 8462.620 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Cell line: BL21 / Plasmid: PET11A / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / 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

DetailsContents: H2O
Sample conditionspH: 6.0 / Temperature: 300 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

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
X-PLOR3.843phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.843BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 25

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