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- PDB-2l56: NMR structure of the GCN4 trigger peptide refined using biased mo... -

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Entry
Database: PDB / ID: 2l56
TitleNMR structure of the GCN4 trigger peptide refined using biased molecular dynamics simulations
ComponentsGeneral control protein GCN4
KeywordsTRANSCRIPTION / GCN4 / COILED-COIL / TRIGGER PEPTIDE / MOLECULAR DYNAMICS SIMULATIONS
MethodSOLUTION NMR / molecular dynamics
Model detailsoccurrence frequencies, model 1
AuthorsMissimer, J.H. / Dolenc, J. / Steinmetz, M.O. / van Gunsteren, W.F.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Molecular basis of coiled-coil formation
Authors: Steinmetz, M.O. / Jelesarov, I. / Matousek, W.M. / Honnappa, S. / Jahnke, W. / Missimer, J.H. / Frank, S. / Alexandrescu, A.T. / Kammerer, R.A.
History
DepositionOct 26, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 26, 2011Group: Other
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 0THIS ENTRY 2L56 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (2OVN.MR) ...THIS ENTRY 2L56 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (2OVN.MR) DETERMINED BY AUTHORS OF THE PDB ENTRY 2OVN: M.O.STEINMETZ,I.JELESAROV,W.M.MATOUSEK,S.HONNAPPA,W.JAHNKE,J.H.MISSIMER,S.FRANK,A.T.ALEXANDRESCU,R.A.KAMMERER. HYDROGEN BOND DISTANCE RESTRAINTS IN 2OVN.MR WERE NOT USED IN THE NEW REFINEMENT PROCEDURE BECAUSE THEY ARE NOT BASED ON THE EXPERIMENTAL NMR DATA.

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Assembly

Deposited unit
A: General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)1,9111
Polymers1,9111
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)10 / 20000conformational cluster analysis
RepresentativeModel #1occurrence frequencies

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Components

#1: Protein/peptide General control protein GCN4


Mass: 1911.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FMOC synthesis
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Processing

NMR softwareName: GROMOS / Version: 53A6 FORCE FIELD / Developer: van Gunsteren and Berendsen / Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: molecular dynamics simulation with time-averaged NOE distance restraining and local elevation biased 3J-value restraining using 179 NOE distances and 15 3J-coupling constants; the 10 ...Details: molecular dynamics simulation with time-averaged NOE distance restraining and local elevation biased 3J-value restraining using 179 NOE distances and 15 3J-coupling constants; the 10 deposited structures were selected from a set of 20000 trajectory configurations by conformational cluster analysis; the occurrence frequencies of the clusters that correspond to the deposited model structures are the following: cluster 1 32% cluster 2 14% cluster 3 6% cluster 4 6% cluster 5 6% cluster 6 3% cluster 7 3% cluster 8 2% cluster 9 2% cluster 10 2%. Authors state that The deviations of the deposited trajectory structures from the so-called "ideal" values for geometrical and stereochemical quantities are partially due to the biasing force derived from the NOE distance bounds and 3J-coupling constants, and partially due to the finite temperature (278K) of the simulations. The ideal geometric and stereochemical values of the GROMOS force field are close to those of Engh and Huber.
NMR representativeSelection criteria: occurrence frequencies
NMR ensembleConformer selection criteria: conformational cluster analysis
Conformers calculated total number: 20000 / Conformers submitted total number: 10 / Representative conformer: 1

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