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- PDB-2arg: FORMATION OF AN AMINO ACID BINDING POCKET THROUGH ADAPTIVE ZIPPER... -

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Entry
Database: PDB / ID: 2arg
TitleFORMATION OF AN AMINO ACID BINDING POCKET THROUGH ADAPTIVE ZIPPERING-UP OF A LARGE DNA HAIRPIN LOOP, NMR, 9 STRUCTURES
ComponentsDNA APTAMER [5'-D (*TP*GP*AP*CP*CP*AP*GP*GP*GP*CP*AP*AP*AP*CP*GP*GP*TP*AP* GP*GP*TP*GP*AP*GP*TP*GP*GP*TP*CP*A)-3']
KeywordsDNA / ADAPTIVE DNA STRUCTURAL TRANSITIONS / L-ARGININAMIDE BINDING POCKET / MOLECULAR RECOGNITION OF AN AMINO ACID / MINOR GROOVE RECOGNITION / BASE ENCAPSULATION WITHIN MINOR GROOVE / DNA APTAMER / DEOXYRIBONUCLEIC ACID
Function / homologyARGININEAMIDE / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY, MOLECULAR DYNAMIC
AuthorsLin, C.H. / Wang, W. / Jones, R.A. / Patel, D.J.
CitationJournal: Chem.Biol. / Year: 1998
Title: Formation of an amino-acid-binding pocket through adaptive zippering-up of a large DNA hairpin loop.
Authors: Lin, C.H. / Wang, W. / Jones, R.A. / Patel, D.J.
History
DepositionAug 19, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Jul 6, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / struct_conn / struct_ref / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair.i_auth_seq_id / _ndb_struct_na_base_pair.i_label_comp_id / _ndb_struct_na_base_pair.i_label_seq_id / _ndb_struct_na_base_pair.j_auth_seq_id / _ndb_struct_na_base_pair.j_label_comp_id / _ndb_struct_na_base_pair.j_label_seq_id / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.pair_name / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_ref.pdbx_align_begin / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1May 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: DNA APTAMER [5'-D (*TP*GP*AP*CP*CP*AP*GP*GP*GP*CP*AP*AP*AP*CP*GP*GP*TP*AP* GP*GP*TP*GP*AP*GP*TP*GP*GP*TP*CP*A)-3']
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5522
Polymers9,3781
Non-polymers1741
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)9 / 20LEAST NOE, VDW, AND BOND ANGLE VIOLATION, LEAST TOTAL ENERGY
Representative

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Components

#1: DNA chain DNA APTAMER [5'-D (*TP*GP*AP*CP*CP*AP*GP*GP*GP*CP*AP*AP*AP*CP*GP*GP*TP*AP* GP*GP*TP*GP*AP*GP*TP*GP*GP*TP*CP*A)-3']


Mass: 9378.040 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: SYNTHESIZED IN-HOUSE ON A 10 MICROMOLAR SCALE SYNTHESIS USING APPLIED BIOSYSTEM 392 DNA/RNA SYNTHESIZER
#2: Chemical ChemComp-AAR / ARGININEAMIDE


Type: L-peptide linking / Mass: 174.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16N5O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131ROESY
1411H-15N HMQC
NMR detailsText: THE INTER-PROTON DISTANCE RESTRAINTS WERE DERIVED FROM 2-D NOE BUILD UP EXPERIMENTS RECORDED AT 50, 90, 150, AND 90 AND 135 MIXING TIME FOR EXCHANGEABLE PROTONS 200 MS MIXING TIME FOR NON- ...Text: THE INTER-PROTON DISTANCE RESTRAINTS WERE DERIVED FROM 2-D NOE BUILD UP EXPERIMENTS RECORDED AT 50, 90, 150, AND 90 AND 135 MIXING TIME FOR EXCHANGEABLE PROTONS 200 MS MIXING TIME FOR NON-EXCHANGEABLE PROTONS AND AT 600 MHZ

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Sample preparation

DetailsContents: 100% D2O
Sample conditionsIonic strength: 100 mM / pH: 6.35 / Pressure: 1 atm / Temperature: 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian VARIAN UNITY PLUS / Manufacturer: Varian / Model: VARIAN UNITY PLUS / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, MOLECULAR DYNAMIC / Software ordinal: 1
Details: TWENTY STARTING STRUCTURES WERE GENERATED BY METRICMATRIX DISTANCE GEOMETRY (FROM X-PLOR) AND WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON ...Details: TWENTY STARTING STRUCTURES WERE GENERATED BY METRICMATRIX DISTANCE GEOMETRY (FROM X-PLOR) AND WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE 2-D NMR DATA SETS. NINE FIN AL NMR-DISTANCE REFINED STRUCTURES WERE SELECTED BASED ON THE CRITERION OF LOW TOTAL ENERGY AND LOW RESTRAINTS VIOLATIONS.
NMR ensembleConformer selection criteria: LEAST NOE, VDW, AND BOND ANGLE VIOLATION, LEAST TOTAL ENERGY
Conformers calculated total number: 20 / Conformers submitted total number: 9

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