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- PDB-143d: SOLUTION STRUCTURE OF THE HUMAN TELOMERIC REPEAT D(AG3[T2AG3]3) O... -

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Entry
Database: PDB / ID: 143d
TitleSOLUTION STRUCTURE OF THE HUMAN TELOMERIC REPEAT D(AG3[T2AG3]3) OF THE G-QUADRUPLEX
ComponentsDNA (5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
KeywordsDNA / HUMAN TELOMERIC SEQUENCE / AG3 REPEAT
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / DISTANCE GEOMETRY, MOLECULAR DYNAMICS
AuthorsWang, Y. / Patel, D.J.
CitationJournal: Structure / Year: 1993
Title: Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex.
Authors: Wang, Y. / Patel, D.J.
History
DepositionOct 8, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Mar 29, 2023Group: Advisory / Derived calculations / Source and taxonomy
Category: database_PDB_caveat / ndb_struct_na_base_pair ...database_PDB_caveat / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_src_syn / struct_conn
Item: _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist ..._ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.i_auth_seq_id_1 / _ndb_struct_na_base_pair_step.i_auth_seq_id_2 / _ndb_struct_na_base_pair_step.i_label_comp_id_1 / _ndb_struct_na_base_pair_step.i_label_comp_id_2 / _ndb_struct_na_base_pair_step.i_label_seq_id_1 / _ndb_struct_na_base_pair_step.i_label_seq_id_2 / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.j_auth_seq_id_1 / _ndb_struct_na_base_pair_step.j_auth_seq_id_2 / _ndb_struct_na_base_pair_step.j_label_comp_id_1 / _ndb_struct_na_base_pair_step.j_label_comp_id_2 / _ndb_struct_na_base_pair_step.j_label_seq_id_1 / _ndb_struct_na_base_pair_step.j_label_seq_id_2 / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.step_name / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,9831
Polymers6,9831
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)6 / 6all calculated structures submitted
Representative

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Components

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


Mass: 6983.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementMethod: DISTANCE GEOMETRY, MOLECULAR DYNAMICS / Software ordinal: 1
Details: A SET OF SIX STRUCTURES WERE OBTAINED USING METRIC MATRIX DISTANCE GEOMETRY, AND SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCES AND ...Details: A SET OF SIX STRUCTURES WERE OBTAINED USING METRIC MATRIX DISTANCE GEOMETRY, AND SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCES AND DIHEDRAL ANGLE RESTRAINTS DERIVED FROM THE NMR DATA. THE SIX DISTANCE-REFINED STRUCTURES WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE FINAL SIX STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 2 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND MINIMIZED. THE R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE SIX FINAL STRUCTURES ARE: MODEL1 MODEL2 MODEL3 MODEL4 MODEL5 MODEL6 R(1/6) FACTOR 0.021 0.016 0.022 0.026 0.024 0.027 BOND (ANG) 0.009 0.008 0.009 0.011 0.009 0.011 ANGLES (DEG) 2.949 3.085 3.286 3.853 3.038 3.157 IMPROPERS (DEG) 0.285 0.221 0.267 0.235 0.243 0.248
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 6 / Conformers submitted total number: 6

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