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- PDB-2l9i: NMR structure of thymosin alpha-1 -

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Basic information

Entry
Database: PDB / ID: 2l9i
TitleNMR structure of thymosin alpha-1
ComponentsThymosin alpha-1
KeywordsPEPTIDE BINDING PROTEIN / LYMPHOCYTE MEMBRANE BINDING PEPTIDE / T-CELL DIFFERENTIATION / IMMUNOPOTENTIATION / TRANSCRIPTION
Function / homology
Function and homology information


histone chaperone activity / chromatin organization / histone binding / DNA-binding transcription factor binding / DNA-templated transcription / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Prothymosin/parathymosin / Prothymosin/parathymosin family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics, restrained molecular dynamics, restrained molecular dynamics, selection, average structure
Model detailsaverage structure, model 1
AuthorsElizondo-Riojas, M.A. / Gorenstein, D.G. / Volk, D.E.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: NMR structure of human thymosin alpha-1.
Authors: Elizondo-Riojas, M.A. / Chamow, S.M. / Tuthill, C.W. / Gorenstein, D.G. / Volk, D.E.
History
DepositionFeb 11, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 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 / pdbx_nmr_software / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thymosin alpha-1


Theoretical massNumber of molelcules
Total (without water)3,0961
Polymers3,0961
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)21 / 10001 average structure + 20 structures with the lowest energy
RepresentativeModel #1average structure

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Components

#1: Protein/peptide Thymosin alpha-1


Mass: 3096.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The protein was made on a protein synthesizer. / Source: (synth.) Homo sapiens (human) / References: UniProt: P06454
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY

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Sample preparation

DetailsContents: 28.8 mg Thymosin-Alpha1, 40 % TFE, 10% D2O, 50% H2O
Solvent system: 10% D2O, 50% H2O
Sample
Conc. (mg/ml)ComponentSolution-ID
28.8 mg/mLThymosin-Alpha1-11
40 %TFE-21
10 %D2O-31
50 %H2O-41
Sample conditionsIonic strength: 0 / pH: 4.9 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian UnityPlus / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmmolecular dynamics
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmminimization
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmdata analysis
Amberrefinement
RefinementMethod: molecular dynamics, restrained molecular dynamics, restrained molecular dynamics, selection, average structure
Software ordinal: 1
Details: 25 ns at 300K on a explicit solvent ratio 40% TFE/H2O (v/v), with a linear-helix initial structure, After the 25 ns on explicit solvent, 1 ns GB simulation follows with all (549)restrains at ...Details: 25 ns at 300K on a explicit solvent ratio 40% TFE/H2O (v/v), with a linear-helix initial structure, After the 25 ns on explicit solvent, 1 ns GB simulation follows with all (549)restrains at 300K., After the 1ns GB restrained simulation, a 10ns restrained MD simulation follows on a explicit solvent ratio 40% TFE/water (v/v). 1000 structures were collected (1 every 10ps), minimized and sorted by total energy. The best 20 structures with the lowest energy were selected., The average structure was obtained from the average of the 20 best structures with the lowest energy and minimized with the 549 restraints and the GB method in order to taking in account the salvation implicitly.
NMR constraintsNOE constraints total: 415 / NOE intraresidue total count: 170 / NOE long range total count: 0 / NOE medium range total count: 106 / NOE sequential total count: 139 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 100 / Protein phi angle constraints total count: 17 / Protein psi angle constraints total count: 17
NMR representativeSelection criteria: average structure
NMR ensembleAverage torsion angle constraint violation: 0.075 °
Conformer selection criteria: 1 average structure + 20 structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 21 / Maximum lower distance constraint violation: 0.033 Å / Maximum torsion angle constraint violation: 4.081 ° / Maximum upper distance constraint violation: 0.368 Å
Torsion angle constraint violation method: minimizing the sum of the absolute values of the errors
NMR ensemble rmsDistance rms dev: 0.0086 Å / Distance rms dev error: 0.036 Å

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