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- PDB-1c95: Solution structure of the aminoacyl-capped oligodeoxyribonucleoti... -

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Basic information

Entry
Database: PDB / ID: 1c95
TitleSolution structure of the aminoacyl-capped oligodeoxyribonucleotide duplex TRP-D(TGCGCAC)2
Components5'-D((5AT)TP*GP*CP*GP*CP*AP*C)-3'
KeywordsDNA / DOUBLE HELIX / Aminoacyl-Capped DNA
Function / homologyTRYPTOPHAN / DNA
Function and homology information
MethodSOLUTION NMR / TORSION-ANGLE MOLECULAR DYNAMICS, CARTESIAN MOLECULAR DYNAMICS
AuthorsHo, W.C. / Steinbeck, C. / Richert, C.
CitationJournal: Biochemistry / Year: 1999
Title: Solution structure of the aminoacyl-capped oligodeoxyribonucleotide duplex (W-TGCGCAC)(2).
Authors: Ho, W.C. / Steinbeck, C. / Richert, C.
History
DepositionJul 31, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D((5AT)TP*GP*CP*GP*CP*AP*C)-3'
B: 5'-D((5AT)TP*GP*CP*GP*CP*AP*C)-3'
A: TRYPTOPHAN
B: TRYPTOPHAN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4434
Polymers4,0352
Non-polymers4082
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D((5AT)TP*GP*CP*GP*CP*AP*C)-3'


Mass: 2017.435 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY
1422D NOESY
152
NMR detailsText: CONSTRAINTS WERE GENERATED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

Details
Solution-IDContents
14 MM TRP-TGCGCAC IN 150 MM NACL AND 10 MM PHOSPHATE BUFFER (KH2PO4/K2HPO4) AT PH 7.0 (UNCORRECTED FOR DEUTERIUM EFFECT)
24 MM TRP-TGCGCAC IN 150 MM NACL AND 10 MM PHOSPHATE BUFFER (KH2PO4/K2HPO4) AT PH 7.0 (UNCORRECTED FOR DEUTERIUM EFFECT)
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1160 mM 7AMBIENT 283 K
2160 mM 7AMBIENT 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
MIT-BUILT5001
MIT-BUILT7502
Bruker DRXBrukerDRX6003
Bruker DPXBrukerDPX3004

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Processing

NMR software
NameVersionDeveloperClassification
RNMR1998RUBEN, D. ET AL. (MIT BITTER LABS)collection
XwinNMR1998BRUKERcollection
Gifa4.1MARC-ANDRE' DELSUC, MONTPELLIER, FRANCEdata analysis
CNS0.4BRUENGER, A.; GROSSE-KUNSTLEVE, R.W. ET AL.; YALE UNIVERSITYstructure solution
X-PLOR3.1BRUENGER, A., ET AL. YALE UNIVERSITYrefinement
RefinementMethod: TORSION-ANGLE MOLECULAR DYNAMICS, CARTESIAN MOLECULAR DYNAMICS
Software ordinal: 1 / Details: SEE TABLE 5 IN PAPER
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers submitted total number: 1

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