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- PDB-5nr6: NMR structure and 1H, 13C and 15N signal assignments for Dictyost... -

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Basic information

Entry
Database: PDB / ID: 5nr6
TitleNMR structure and 1H, 13C and 15N signal assignments for Dictyostelium discoidans MATB protein S71A mutant
ComponentsMatB protein
KeywordsDNA BINDING PROTEIN / Mating type determination factor / Homeobox
Function / homologyMatB protein
Function and homology information
Biological speciesDictyostelium discoideum (eukaryote)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsNeuhaus, D. / Hedgethorne, K. / Yang, J.-C.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105178934 United Kingdom
Medical Research Council (United Kingdom)MC_U105115237 United Kingdom
CitationJournal: Sci Adv / Year: 2017
Title: Homeodomain-like DNA binding proteins control the haploid-to-diploid transition in Dictyostelium.
Authors: Hedgethorne, K. / Eustermann, S. / Yang, J.C. / Ogden, T.E.H. / Neuhaus, D. / Bloomfield, G.
History
DepositionApr 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MatB protein


Theoretical massNumber of molelcules
Total (without water)12,6521
Polymers12,6521
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11460 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein MatB protein


Mass: 12652.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: matB / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3UFE5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
132isotropic12D 1H-13C HSQC aliphatic
142isotropic23D HN(CA)CB
152isotropic23D CBCA(CO)NH
162isotropic23D HNHAHB
172isotropic23D HBHA(CO)NH
182isotropic23D [1H-13C-1H] (H)CCH-TOCSY
192isotropic23D [13C-13C-1H] (H)CCH-TOCSY
1102isotropic23D [1H-13C-1H] (H)CCH-COSY
1112isotropic23D 1H-15N NOESY (mix. time 150ms)
1122isotropic23D 1H-13C NOESY aliphatic (mix. time 150ms)
1132isotropic23D 1H-13C NOESY aromatic (mix. time 150ms)

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1600 uM [U-15N] MATB, 25 mM sodium phosphate, 100 mM sodium chloride, 50 uM EDTA, 95% H2O/5% D2O15N_sample95% H2O/5% D2O
solution2600 uM [U-13C; U-15N] MATB, 25 mM sodium phosphate, 100 mM sodium chloride, 50 uM EDTA, 95% H2O/5% D2O15N,13C_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMMATB[U-15N]1
25 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
50 uMEDTAnatural abundance1
600 uMMATB[U-13C; U-15N]2
25 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
50 uMEDTAnatural abundance2
Sample conditionsIonic strength: 100mM NaCl, 25mM Na3PO4 Not defined / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 274 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1 and 3.2Bruker Biospinprocessing
CcpNmr Analysis2.4CCPNchemical shift assignment
UNIO2.0.3Herrmannstructure calculation
Xplor-NIH2.28Schwieters, Kuszewski, Tjandra and Clorestructure calculation
Amber11Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Refinement
MethodSoftware ordinal
simulated annealing3
simulated annealing4
molecular dynamics5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 30

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