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- PDB-2kn8: NMR structure of the C-terminal domain of pUL89 -

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Basic information

Entry
Database: PDB / ID: 2kn8
TitleNMR structure of the C-terminal domain of pUL89
ComponentsDNA cleavage and packaging protein large subunit, UL89
KeywordsPROTEIN BINDING / DNA BINDING PROTEIN / NHCMV / pUL89 / Terminase
Function / homology
Function and homology information


chromosome organization => GO:0051276 / nuclease activity / viral release from host cell / Hydrolases; Acting on ester bonds / membrane => GO:0016020 / host cell nucleus / DNA binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #480 / Probable DNA packing protein, C-terminal / Probable DNA packing protein, N-terminal / Tripartite terminase subunit 3 / Probable DNA packing protein, C-terminal domain superfamily / Probable DNA packing protein, C-terminus / Probable DNA packing protein, N-terminus / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Tripartite terminase subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing
Model detailslowest energy, model 1
AuthorsCouvreux, A. / Hantz, S. / Marquant, R. / Champier, G. / Alain, S. / Morellet, N. / Bouaziz, S.
CitationJournal: Proteins / Year: 2010
Title: Insight into the structure of the pUL89 C-terminal domain of the human cytomegalovirus terminase complex.
Authors: Couvreux, A. / Hantz, S. / Marquant, R. / Champier, G. / Alain, S. / Morellet, N. / Bouaziz, S.
History
DepositionAug 18, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA cleavage and packaging protein large subunit, UL89


Theoretical massNumber of molelcules
Total (without water)7,9171
Polymers7,9171
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA cleavage and packaging protein large subunit, UL89 / DNA packaging terminase subunit 1


Mass: 7916.908 Da / Num. of mol.: 1 / Fragment: sequence database residues 568-635 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6RXE9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of the C-terminal domain of pUL89 from human cytomegalovirus terminase complex
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D DQF-COSY
1312D 1H-1H NOESY
1412D 1H-1H TOCSY
1513D 1H-15N NOESY
1613D 1H-15N TOCSY

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Sample preparation

DetailsContents: 0.8 mM pUL89-Cter, 50% H2O / 50% acetonitril (v/v)
Solvent system: 50% H2O / 50% acetonitril (v/v)
SampleConc.: 0.8 mM / Component: pUL89-Cter-1
Sample conditionspH: 3.2 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorerefinement
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: 10

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