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- PDB-2km1: Solution structure of the N-terminal domain of the yeast protein Dre2 -

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Basic information

Entry
Database: PDB / ID: 2km1
TitleSolution structure of the N-terminal domain of the yeast protein Dre2
ComponentsProtein DRE2
KeywordsPROTEIN BINDING / Dre2 / yeast / antiapoptotic
Function / homology
Function and homology information


negative regulation of hydrogen peroxide-mediated programmed cell death / negative regulation of nitric oxide biosynthetic process / iron-sulfur cluster assembly / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Fe-S cluster assembly protein Dre2, N-terminal domain / Fe-S cluster assembly protein Dre2, N-terminal / Fe-S cluster assembly protein DRE2 N-terminus / Anamorsin / Cytokine-induced anti-apoptosis inhibitor 1, Fe-S biogenesis / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Fe-S cluster assembly protein DRE2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsCraescu, C.T. / Soler, N. / Delagoutte, E. / Baldacci, G. / Vernis-Beringue, L.
CitationJournal: Febs J. / Year: 2012
Title: A S-adenosylmethionine methyltransferase-like domain within the essential, Fe-S containing yeast protein Dre2
Authors: Soler, N. / Craescu, C.T. / Gallay, J. / Frapart, Y.M. / Mansuy, D. / Raynal, B. / Baldacci, G. / Pastore, A. / Huang, M.E. / Vernis, L.
History
DepositionJul 16, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Structure summary
Revision 1.3May 9, 2012Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein DRE2


Theoretical massNumber of molelcules
Total (without water)15,1401
Polymers15,1401
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 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein DRE2


Mass: 15140.460 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YKR071C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36152

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY
1422D 1H-1H TOCSY
1522D 1H-1H NOESY
1622D DQF-COSY
1712D 1H-15N HSQC
1813D 1H-15N NOESYHSQC
1913D 1H-15N TOCSYHSQC
11013D HNCO
11113D HN(CA)CO
11213D HNCA
11313D HN(CO)CA
11413D HN(CA)CB
11523D 1H-13C NOESY
11623D 1H-13 (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM N-Dre2, 1mM [U-99% 2H] DTT, 100mM sodium chloride, 50mM sodium phosphate, 93% H2O/7% D2O93% H2O/7% D2O
21mM N-Dre2, 1mM [U-99% 2H] DTT, 100mM sodium chloride, 50mM sodium phosphate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMN-Dre2-11
1 mMDTT-2[U-99% 2H]1
100 mMsodium chloride-31
50 mMsodium phosphate-41
1 mMN-Dre2-52
1 mMDTT-6[U-99% 2H]2
100 mMsodium chloride-72
50 mMsodium phosphate-82
Sample conditionsIonic strength: 0.2 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityVarianUNITY5001
Bruker AMXBrukerAMX6002

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Processing

NMR software
NameVersionDeveloperClassification
DiscoverI2005Accelrys Software Inc.structure solution
Felix2000.1Accelrys Software Inc.chemical shift assignment
DiscoverI2005Accelrys Software Inc.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Simulated annealing under experimental restraints and the force field cvff
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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