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- PDB-1kjk: Solution structure of the lambda integrase amino-terminal domain -

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Basic information

Entry
Database: PDB / ID: 1kjk
TitleSolution structure of the lambda integrase amino-terminal domain
Componentsintegrase
KeywordsVIRAL PROTEIN / DNA recombination / integrase / three-stranded beta-sheet / DNA-binding domain
Function / homology
Function and homology information


provirus excision / integrase activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / DNA recombination / Hydrolases; Acting on ester bonds / hydrolase activity ...provirus excision / integrase activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / DNA recombination / Hydrolases; Acting on ester bonds / hydrolase activity / symbiont entry into host cell / DNA binding
Similarity search - Function
Integrase, lambda-type, N-terminal DNA-binding / Bacteriophage lambda integrase, Arm DNA-binding domain / Phage integrase, N-terminal SAM-like domain / Integrase, SAM-like, N-terminal / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Phage integrase family / Integrase, catalytic domain / Integrase/recombinase, N-terminal ...Integrase, lambda-type, N-terminal DNA-binding / Bacteriophage lambda integrase, Arm DNA-binding domain / Phage integrase, N-terminal SAM-like domain / Integrase, SAM-like, N-terminal / 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
Biological speciesEnterobacteria phage lambda (virus)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsWojciak, J.M. / Sarkar, D. / Landy, A. / Clubb, R.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Arm-site binding by lambda -integrase: solution structure and functional characterization of its amino-terminal domain.
Authors: Wojciak, J.M. / Sarkar, D. / Landy, A. / Clubb, R.T.
History
DepositionDec 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 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: integrase


Theoretical massNumber of molelcules
Total (without water)7,6291
Polymers7,6291
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)25 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein integrase


Mass: 7628.709 Da / Num. of mol.: 1 / Fragment: amino-terminal domain (residues 1-64)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Plasmid: pIMC104 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03700

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131quantitative J correlation

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Sample preparation

DetailsContents: 1mM integrase U-15N,13C; 20mM PO4 (pH 6.0), 100mM NaCl, 10mM DTT, 0.01% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.0 / Pressure: 1 atm / Temperature: 290 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipesgi6xDelaglioprocessing
PIPP/CAPP/STAPP4.1.2Garrettdata analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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