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- PDB-2wcc: phage lambda IntDBD1-64 complex with p prime 2 DNA -

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Basic information

Entry
Database: PDB / ID: 2wcc
Titlephage lambda IntDBD1-64 complex with p prime 2 DNA
Components
  • DNA (5'-D(*DCP*DGP*DAP*DGP*DTP*DCP*DAP *DAP*DAP*DAP*DTP*DC)-3')
  • DNA (5'-D(*DGP*DAP*DTP*DTP*DTP*DTP*DGP *DAP*DCP*DTP*DGP*DC)-3')
  • INTEGRASE
KeywordsPROTEIN/DNA / DNA INTEGRATION / DNA RECOMBINATION / EXCISION / INTEGRATION / PHAGE LAMBDA / RECOMBINATION / PROTEIN DNA COMPLEX / PROTEIN-DNA complex
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 / : / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. ...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 / : / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. / 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) / Integrase
Similarity search - Component
Biological speciesENTEROBACTERIA PHAGE LAMBDA (virus)
MethodSOLUTION NMR / MARS, QUEEN, ATNOS CANDID
AuthorsFadeev, E.A. / Sam, M.D. / Clubb, R.T.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: NMR Structure of the Amino-Terminal Domain of the Lambda Integrase Protein in Complex with DNA: Immobilization of a Flexible Tail Facilitates Beta- Sheet Recognition of the Major Groove.
Authors: Fadeev, E.A. / Sam, M.D. / Clubb, R.T.
History
DepositionMar 11, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: DNA (5'-D(*DCP*DGP*DAP*DGP*DTP*DCP*DAP *DAP*DAP*DAP*DTP*DC)-3')
2: DNA (5'-D(*DGP*DAP*DTP*DTP*DTP*DTP*DGP *DAP*DCP*DTP*DGP*DC)-3')
3: INTEGRASE


Theoretical massNumber of molelcules
Total (without water)14,9533
Polymers14,9533
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 / 200LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: DNA chain DNA (5'-D(*DCP*DGP*DAP*DGP*DTP*DCP*DAP *DAP*DAP*DAP*DTP*DC)-3')


Mass: 3655.419 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: INTN(1-64) COMPLEX WITH 12 MER DOUBLE STRANDED P'2 DNA
Source: (synth.) ENTEROBACTERIA PHAGE LAMBDA (virus)
#2: DNA chain DNA (5'-D(*DGP*DAP*DTP*DTP*DTP*DTP*DGP *DAP*DCP*DTP*DGP*DC)-3')


Mass: 3668.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: INTN(1-64) COMPLEX WITH 12 MER DOUBLE STRANDED P'2 DNA
Source: (synth.) ENTEROBACTERIA PHAGE LAMBDA (virus)
#3: Protein INTEGRASE / PHAGE LAMBDA INTN-DNA COMPLEX


Mass: 7628.709 Da / Num. of mol.: 1 / Fragment: P'2 DNA BINDING DOMAIN, RESIDUES 1-64
Source method: isolated from a genetically manipulated source
Details: INTN(1-64) COMPLEX WITH 12 MER DOUBLE STRANDED P'2 DNA
Source: (gene. exp.) ENTEROBACTERIA PHAGE LAMBDA (virus) / Production host: ESCHERICHIA COLI (E. coli) / 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
11115N HSQC
12113 HSQC
1313D 15N NOESY
1413D 15N TOCSY
151HNCO
161HNCA
171HN(CA)CB
181CBCA(CO)NH
191HNHB
1101HNHA
1111HN(CA)CO
1121(H)CCH COSY
1131(H)CCH TOCSY
11413D 13C EDITED NOESY
11512D F1F2 13C FILTERED NOESY
11612D F1 13C FILTERED NOESY
117113C F1
1181F2 FILTERED NOESY
119113C F1 FILTERED NOESY
NMR detailsText: STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR EXPERIMENTS ON 13C 15N LABELED PROTEIN, UNLABELED DNA. INTERMOLECULAR NOES WERE MEASURED USING 13C FILTERED 2D NOESY ,13C-EDITED 3D NOESY AND ...Text: STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR EXPERIMENTS ON 13C 15N LABELED PROTEIN, UNLABELED DNA. INTERMOLECULAR NOES WERE MEASURED USING 13C FILTERED 2D NOESY ,13C-EDITED 3D NOESY AND 15N-EDITED 3D NOESY EXPERIMENTS

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Sample preparation

DetailsContents: 7% D2O 93% WATER
Sample conditionsIonic strength: 40 mM / pH: 7 / Pressure: 1.0 atm / Temperature: 310.15 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.14SCHWIETERS, KUSZEWSKI, TJrefinement
Sparkystructure solution
RefinementMethod: MARS, QUEEN, ATNOS CANDID / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 200 / Conformers submitted total number: 20

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