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- PDB-1j9i: STRUCTURE OF THE DNA BINDING DOMAIN OF THE GPNU1 SUBUNIT OF LAMBD... -

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Basic information

Entry
Database: PDB / ID: 1j9i
TitleSTRUCTURE OF THE DNA BINDING DOMAIN OF THE GPNU1 SUBUNIT OF LAMBDA TERMINASE
ComponentsTERMINASE SMALL SUBUNIT
KeywordsVIRAL PROTEIN / DNA BINDING DOMAIN / HOMODIMER / VIRAL ASSEMBLY / LAMBDA / WINGED HELIX-TURN-HELIX / TERMINASE
Function / homology
Function and homology information


viral terminase, small subunit / sequence-specific DNA binding, bending / viral DNA genome packaging / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / host cell cytoplasm / ATP hydrolysis activity / ATP binding
Similarity search - Function
Bacteriophage lambda, Nu1, terminase small subunit / Phage DNA packaging protein Nu1 / Putative DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Terminase small subunit
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodSOLUTION NMR / simulated annealing
AuthorsDe Beer, T. / Meyer, J. / Ortega, M. / Yang, Q. / Maes, L. / Duffy, C. / Berton, N. / Sippy, J. / Overduin, M. / Feiss, M. / Catalano, C.
CitationJournal: Mol.Cell / Year: 2002
Title: Insights into specific DNA recognition during the assembly of a viral genome packaging machine.
Authors: de Beer, T. / Fang, J. / Ortega, M. / Yang, Q. / Maes, L. / Duffy, C. / Berton, N. / Sippy, J. / Overduin, M. / Feiss, M. / Catalano, C.E.
History
DepositionMay 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TERMINASE SMALL SUBUNIT
B: TERMINASE SMALL SUBUNIT


Theoretical massNumber of molelcules
Total (without water)15,6382
Polymers15,6382
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein TERMINASE SMALL SUBUNIT / DNA PACKAGING PROTEIN NU1 / GPNU1 DBD


Mass: 7818.768 Da / Num. of mol.: 2 / Fragment: DNA BINDING DOMAIN, RESIDUES 1-68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Gene: NU1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03707

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
1333D 15N-separated NOESY
143HNHA
1543D 13C-separated NOESY
1644D 13C-separated NOESY
1753D 13C-separated NOESY
1862D half-filtered 13C/15N NOESY
NMR detailsText: mixing times were 50 or 100 ms

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM homonuclear gpNu1 DBD90% H2O/10% D2O
21 mM homonuclear gpNu1 DBD99.99 % D2O
31 mM {15N} gpNu1 DBD90% H2O/10% D2O
41 mM {13C,15N} gpNu1 DBD99.99 % D2O
51 mM {13C,15N} gpNu1 DBD90% H2O/10% D2O
61 mM 50%/50% {13C,15N} gpNu1 DBD/{12C,14N}gpNu1 DBD90% H2O/10% D2O
Sample conditionsIonic strength: 20 mM deuterated TRIS / pH: 6.0 / Pressure: AMBIENT / Temperature: 298.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1Delaglio et al.processing
NMRView5Johnson et al.data analysis
PIPP1Garrett et al.data analysis
X-PLOR3.851BRUNGER ET AL.structure solution
X-PLOR3.851BRUNGER ET AL.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE R-6 SUMMATION METHOD WAS USED WITHIN A SIMULATED ANNEALING PROTOCOL.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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