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- PDB-2mqk: Solution structure of N terminal domain of the MuB AAA+ ATPase -

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Basic information

Entry
Database: PDB / ID: 2mqk
TitleSolution structure of N terminal domain of the MuB AAA+ ATPase
ComponentsATP-dependent target DNA activator B
KeywordsHYDROLASE
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
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 domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / AAA+ ATPase domain / 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 / torsion angle dynamics
Model detailsfewest violations, model1
AuthorsLopez-Mendez, B. / Dramicanin, M. / Campos-Olivas, R. / Ramon-Maiques, S.
CitationJournal: To be Published
Title: Solution structure of N terminal domain of the MuB AAA+ ATPase
Authors: Dramicanin, M. / Lopez-Mendez, B. / Campos-Olivas, R. / Ramon-Maiques, S.
History
DepositionJun 23, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent target DNA activator B


Theoretical massNumber of molelcules
Total (without water)7,3531
Polymers7,3531
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein ATP-dependent target DNA activator B / Gene product B / gpB / MuB


Mass: 7353.117 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-63 / Mutation: M53T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Mu (virus) / Gene: B, Mup04 / Production host: Escherichia coli (E. coli) / References: UniProt: P03763, EC: 3.6.1.3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1223D 1H-15N NOESY
1323D HNHA
1412D 1H-1H TOCSY
1512D 1H-1H NOESY
1612D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
1500 uM MuB-NTD-1, 20 mM sodium phosphate-2, 100 mM sodium chloride-3, 93% H2O/7% D2O93% H2O/7% D2O
2500 uM [U-98% 15N] MuB-NTD-4, 20 mM sodium phosphate-5, 100 mM sodium chloride-6, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMMuB-NTD-11
20 mMsodium phosphate-21
100 mMsodium chloride-31
500 uMMuB-NTD-4[U-98% 15N]2
20 mMsodium phosphate-52
100 mMsodium chloride-62
Sample conditionsIonic strength: 100 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.2.6Guntert, Mumenthaler and Wuthrichstructure solution
OPAL1.4Luginbuhl, Guntert, Billeter and Wuthrichrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CCPN2.3.1CCPNdata analysis
CCPN2.3.1CCPNchemical shift assignment
CCPN2.3.1CCPNpeak picking
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
TALOS+Cornilescu, Delaglio and Baxbackbone torsion angle restraint generation
CYANAGUNTERT, MUMENTHALER AND WUTHRICHrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1518 / NOE intraresidue total count: 356 / NOE long range total count: 432 / NOE medium range total count: 390 / NOE sequential total count: 340 / Protein phi angle constraints total count: 46 / Protein psi angle constraints total count: 46
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 2 ° / Maximum upper distance constraint violation: 0.16 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.0105 Å / Distance rms dev error: 0.0004 Å

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