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- PDB-2mxf: Structure of the DNA complex of the C-Terminal domain of MvaT -

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Basic information

Entry
Database: PDB / ID: 2mxf
TitleStructure of the DNA complex of the C-Terminal domain of MvaT
Components
  • 5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*TP*GP*CP*G)-3'
  • MvaT
KeywordsTRANSCRIPTION REGULATOR/DNA / TRANSCRIPTION REGULATOR-DNA complex
Function / homology
Function and homology information


negative regulation of single-species biofilm formation on inanimate substrate / negative regulation of secondary metabolite biosynthetic process / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription
Similarity search - Function
MvaT, DNA-binding domain / Bacterial xenogeneic silencer MvaT, C-terminal domain
Similarity search - Domain/homology
DNA / DNA (> 10) / MvaT
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsDing, P. / Xia, B.
CitationJournal: Plos Pathog. / Year: 2015
Title: A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT.
Authors: Ding, P. / McFarland, K.A. / Jin, S. / Tong, G. / Duan, B. / Yang, A. / Hughes, T.R. / Liu, J. / Dove, S.L. / Navarre, W.W. / Xia, B.
History
DepositionDec 30, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: MvaT
B: 5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*TP*GP*CP*G)-3'
C: 5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*TP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)13,7853
Polymers13,7853
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2848 Å2
ΔGint-5.2 kcal/mol
Surface area6575 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein MvaT / Transcriptional regulator MvaT / P16 subunit


Mass: 6460.413 Da / Num. of mol.: 1 / Fragment: C-Terminal domain (UNP residues 77-124)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: mvaT, PA4315 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HW86
#2: DNA chain 5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*TP*GP*CP*G)-3'


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D (H)CCH-TOCSY
1313D (H)CCH-COSY
1413D 1H-15N NOESY
1513D 1H-13C NOESY
1612D 1H-1H NOESY
1712D 1H-1H TOCSY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] MvaT, 50 mM sodium phosphate, 50 mM sodium chloride, 1 mM DNA (5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*TP*GP*CP*G)-3'), 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMvaT-1[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate-21
50 mMsodium chloride-31
1 mMDNA (5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*TP*GP*CP*G)-3')-41
Sample conditionsIonic strength: 0.1 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR softwareName: Amber
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
Classification: refinement
RefinementMethod: 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: 20

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