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- PDB-2mbf: Solution structure of the forkhead domain of Brugia malayi DAF-16a -

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Basic information

Entry
Database: PDB / ID: 2mbf
TitleSolution structure of the forkhead domain of Brugia malayi DAF-16a
ComponentsFork head domain containing protein
KeywordsTRANSCRIPTION / forkhead / FOXO / FOXO3a / winged helix / insulin/IGF-1 signaling / filarial parasites
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesBrugia malayi (agent of lymphatic filariasis)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsVeldkamp, C.T. / Peterson, F.C. / Casper, S.K. / Schoeller, S.J.
CitationJournal: Proteins / Year: 2014
Title: The solution structure of the forkhead box-O DNA binding domain of Brugia malayi DAF-16a.
Authors: Casper, S.K. / Schoeller, S.J. / Zgoba, D.M. / Phillips, A.J. / Morien, T.J. / Chaffee, G.R. / Sackett, P.C. / Peterson, F.C. / Crossgrove, K. / Veldkamp, C.T.
History
DepositionJul 30, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Oct 29, 2014Group: Database references
Revision 1.3Dec 10, 2014Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Fork head domain containing protein


Theoretical massNumber of molelcules
Total (without water)11,6731
Polymers11,6731
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Fork head domain containing protein


Mass: 11672.978 Da / Num. of mol.: 1 / Fragment: UNP residues 342-442
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: Bm1_50095 / Production host: Escherichia coli (E. coli) / References: UniProt: A8QCW6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)

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Sample preparation

DetailsContents: 0.5 mM [U-98% 13C; U-98% 15N] Forkhead box DNA binding domain of Brugia malayi DAF-16a, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM
Component: Forkhead box DNA binding domain of Brugia malayi DAF-16a-1
Isotopic labeling: [U-98% 13C; U-98% 15N]
Sample conditionsIonic strength: 200 / pH: 6.0 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
TopSpin2.1Brukercollection
NMRPipe2007Delagio,F. et al.processing
XEASY1.3Eccles, C., Guntert, P., Billeter, M., Wuthrich, K.data analysis
GARANT2.1C. Bartelsdata analysis
CARA1.8.4Keller, R.data analysis
CYANA3Guntert, P.structural calculation
CYANA3Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT. Bm-DAF-16a ...Details: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT. Bm-DAF-16a STRUCTURES ARE BASED ON A TOTAL OF 29521 NOE CONSTRAINTS ( 1771 INTRA, 455 SEQUENTIAL, 415 MEDIUM, 313 LONG RANGE) AND 114 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS., Bm-DAF-16a STRUCTURES ARE BASED ON A TOTAL OF 29521 NOE CONSTRAINTS ( 1771 INTRA, 455 SEQUENTIAL, 415 MEDIUM, 313 LONG RANGE) AND 114 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR constraintsNOE constraints total: 2954 / NOE intraresidue total count: 1771 / NOE long range total count: 313 / NOE medium range total count: 415 / NOE sequential total count: 455
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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