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- PDB-1ekh: NMR STRUCTURE OF D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A3 AND COBALT -

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Basic information

Entry
Database: PDB / ID: 1ekh
TitleNMR STRUCTURE OF D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A3 AND COBALT
ComponentsDNA (5'-D(*TP*TP*GP*GP*CP*CP*AP*A)-3')
KeywordsDNA / drug bound in the minor groove of DNA
Function / homology: / Chem-CPH / DNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsGochin, M.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: A high-resolution structure of a DNA-chromomycin-Co(II) complex determined from pseudocontact shifts in nuclear magnetic resonance.
Authors: Gochin, M.
#1: Journal: J.Am.Chem.Soc. / Year: 1999
Title: Structure determination by restrained molecular dynamics using NMR pseudocontact shifts as experimentally determined constraints
Authors: Tu, K. / Gochin, M.
History
DepositionMar 8, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionMar 20, 2000ID: 1CQB
Revision 1.0Mar 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2011Group: Advisory
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nmr_software / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nmr_software.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,3519
Polymers4,8532
Non-polymers2,4977
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)6 / 100MINIMIZED AVERAGED COORDINATES FROM 6 RUNS
Representative

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Components

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


Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: TWO MOLECULES OF THE DRUG CHROMOMYCIN A3 (1GL-2GL-DXB-DDA-DDA-1AR, CHAINS C, AND D) ARE BOUND IN THE MINOR GROOVE
#2: Polysaccharide 2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-4-O-acetyl-2,6-dideoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 334.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ad112m-1b_1-5_4*OCC/3=O][ad112m-1a_1-5_4*OC]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-2-deoxy-Fucp4Ac]{[(3+1)][a-D-2-deoxy-Fucp4Me]{}}LINUCSPDB-CARE
#3: Polysaccharide 3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-beta-D-Olivopyranose-(1-3)-beta-D-Olivopyranose


Type: oligosaccharide / Mass: 464.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[ad122m-1b_1-5][ad611m-1a_1-5_3*C_4*OCC/3=O]/1-1-2/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-2,6-deoxy-Glcp]{[(3+1)][b-D-2,6-deoxy-Glcp]{[(3+1)][a-L-2,6-deoxy-Glcp4Ac]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-CPH / (1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose / None


Mass: 420.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24O9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING PSEUDOCONTACT SHIFTS IN THE NMR SPECTRUM. PSEUDOCONTACT SHIFTS WERE MEASURED AS THE DIFFERENCE IN THE CHEMICAL SHIFT BETWEEN THE CO(II) COMPLEX AND THE ZN(II) ...Text: THE STRUCTURE WAS DETERMINED USING PSEUDOCONTACT SHIFTS IN THE NMR SPECTRUM. PSEUDOCONTACT SHIFTS WERE MEASURED AS THE DIFFERENCE IN THE CHEMICAL SHIFT BETWEEN THE CO(II) COMPLEX AND THE ZN(II) COMPLEX. IN MODELS 1-3, ONLY SHIFTS WERE USED; IN MODELS 4-6 SHIFTS + NOE'S WERE USED IN REFINEMENT.

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Sample preparation

DetailsContents: D2O, 90% H2O, 10% D2O
Sample conditionsIonic strength: 100mM NACL / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: GE OMEGA500 / Manufacturer: GE / Model: OMEGA500 / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.7DeLaglio and Baxprocessing
Sparky3Kneller and Goddarddata analysis
X-PLOR3.0, 3.851Brunger (modified by Gochin and Tu)refinement
Felix2.1Biosymdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Paramagnetic Shifts and NOEs used in refinement. Other REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: MINIMIZED AVERAGED COORDINATES FROM 6 RUNS
Conformers calculated total number: 100 / Conformers submitted total number: 6

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