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- PDB-1f6v: SOLUTION STRUCTURE OF THE C TERMINAL OF MU B TRANSPOSITION PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1f6v
TitleSOLUTION STRUCTURE OF THE C TERMINAL OF MU B TRANSPOSITION PROTEIN
ComponentsDNA TRANSPOSITION PROTEIN
KeywordsDNA BINDING PROTEIN / Mu phage / recombination / transposition / ATPase / DNA binding / high salt / solution structure
Function / homology
Function and homology information


DNA transposition / viral DNA genome replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / DNA integration / host cell cytoplasm / DNA replication / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
DNA Transposition Protein; Chain A / B transposition protein, C-terminal domain / B transposition protein, C-terminal / B transposition protein, C-terminal domain superfamily / Mu B transposition protein, C terminal / : / : / AAA domain / Lambda repressor-like, DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase ...DNA Transposition Protein; Chain A / B transposition protein, C-terminal domain / B transposition protein, C-terminal / B transposition protein, C-terminal domain superfamily / Mu B transposition protein, C terminal / : / : / AAA domain / Lambda repressor-like, DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ATP-dependent target DNA activator B
Similarity search - Component
Biological speciesEnterobacteria phage Mu (virus)
MethodSOLUTION NMR / simulated annealing
AuthorsHung, L.-H. / Chaconas, G. / Shaw, G.S.
CitationJournal: EMBO J. / Year: 2000
Title: The solution structure of the C-terminal domain of the Mu B transposition protein.
Authors: Hung, L.H. / Chaconas, G. / Shaw, G.S.
History
DepositionJun 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA TRANSPOSITION PROTEIN


Theoretical massNumber of molelcules
Total (without water)10,2381
Polymers10,2381
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 / 100structures with lowest energy and no restraint violations with phi psi angles in allowed regions
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA TRANSPOSITION PROTEIN / MU B TRANSPOSITION PROTEIN


Mass: 10237.761 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Mu (virus) / Genus: Mu-like viruses / Description: T7 PHAGE / Plasmid: PHH05 / Production host: Escherichia coli (E. coli) / References: UniProt: P03763

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
132HNHA
1423D 15N-separated TOCSY
1532D NOESY
1632D TOCSY
17415N-HSQC
NMR detailsText: High ionic conditions precluded many of the standard triple resonance experiments.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.75 mM Mu B U-15N,13C; 20 mM phosphate buffer100% D2O
20.75 mM Mu B U-15N; 20 mM phosphate buffer90% H20, 10% D2O
30.75 mM Mu B NA; 20 mM phosphate buffer100% D2O
4Mu B U-15N-(combinations of Leu, Ile, Gly, Ser, Glu, Arg, Ala),20 mM phosphate buffer90% H20, 10% D2O
Sample conditionsIonic strength: 1.5 M NaCl / pH: 6.8 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerrefinement
NMRPipeDelaglioprocessing
VNMRcollection
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1047 NOE derived, and 55 dihedral constraints. There are no long-range NOEs observed for the first 8 residues which are disordered.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with lowest energy and no restraint violations with phi psi angles in allowed regions
Conformers calculated total number: 100 / Conformers submitted total number: 20

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