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- PDB-207d: SOLUTION STRUCTURE OF MITHRAMYCIN DIMERS BOUND TO PARTIALLY OVERL... -

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Basic information

Entry
Database: PDB / ID: 207d
TitleSOLUTION STRUCTURE OF MITHRAMYCIN DIMERS BOUND TO PARTIALLY OVERLAPPING SITES ON DNA
ComponentsDNA (5'-D(*TP*AP*GP*CP*TP*AP*GP*CP*TP*A)-3')
KeywordsDNA / DOUBLE HELIX / MITHRAMYCIN
Function / homologyChem-CRH / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsSastry, M. / Fiala, R. / Patel, D.J.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: Solution structure of mithramycin dimers bound to partially overlapping sites on DNA.
Authors: Sastry, M. / Fiala, R. / Patel, D.J.
History
DepositionApr 20, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1May 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 24, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / ndb_struct_na_base_pair / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_ref / struct_ref_seq
Item: _chem_comp.type / _ndb_struct_na_base_pair.propeller ..._chem_comp.type / _ndb_struct_na_base_pair.propeller / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag
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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / 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.pdbx_PDB_ins_code / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _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.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.value / _pdbx_validate_close_contact.PDB_ins_code_1 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.pdbx_value_order / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)10,49316
Polymers6,0882
Non-polymers4,40514
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10480 Å2
ΔGint114 kcal/mol
Surface area2380 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 8all calculated structures submitted
Representative

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Components

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


Mass: 3044.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Source: (synth.) synthetic construct (others)
#2: Polysaccharide
beta-D-Olivopyranose-(1-3)-beta-D-Olivopyranose


Type: oligosaccharide / Mass: 278.299 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DOlib1-3DOlib1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[ad122m-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-2,6-deoxy-Glcp]{[(3+1)][b-D-2,6-deoxy-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide
2,6-dideoxy-3-C-methyl-beta-D-ribo-hexopyranose-(1-3)-2,6-dideoxy-beta-D-galactopyranose-(1-3)-beta- ...2,6-dideoxy-3-C-methyl-beta-D-ribo-hexopyranose-(1-3)-2,6-dideoxy-beta-D-galactopyranose-(1-3)-beta-D-Olivopyranose


Type: oligosaccharide / Mass: 422.468 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/3,3,2/[ad122m-1b_1-5][ad112m-1b_1-5][ad622m-1b_1-5_3*C]/1-2-3/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-2,6-deoxy-Glcp]{[(3+1)][b-D-2-deoxy-Fucp]{[(3+1)][b-D-2,6-deoxy-Allp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CRH / 1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYROXY-7-METHYLANTHRACENE


Mass: 388.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H24O7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: EACH MODEL CONTAINS FOUR MOLECULES OF MITHRAMYCIN (EACH WITH FORMULA C52 H75 O24, CHARGE -1) AND TWO MG++ CATIONS THAT COORDINATE TO TWO MITHRAMYCIN MOLECULES. IN THIS ENTRY MITHRAMYCIN IS ...Text: EACH MODEL CONTAINS FOUR MOLECULES OF MITHRAMYCIN (EACH WITH FORMULA C52 H75 O24, CHARGE -1) AND TWO MG++ CATIONS THAT COORDINATE TO TWO MITHRAMYCIN MOLECULES. IN THIS ENTRY MITHRAMYCIN IS PRESENTED AS HET GROUPS DDA-DDA-CHR- TSC. THE TSC RESIDUE IS COMPRISED OF THREE SACCHARIDE UNITS (DDA-DDL-MDA). THE HYDROPHILIC SIDE CHAIN AND THE A-B DISACCHARIDE OF MITHRAMYCIN MOLECULES ALONG WITH THE TERMINAL BASE PAIR IN THE DNA DUPLEX ARE NOT WELL DEFINED.

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: TWO STARTING STRUCTURES WERE OBTAINED BY MANUALLY DOCKING MITHRAMYCIN ON A FORM AND B FORM DNA. THESE WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER- ...Details: TWO STARTING STRUCTURES WERE OBTAINED BY MANUALLY DOCKING MITHRAMYCIN ON A FORM AND B FORM DNA. THESE WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCES DERIVED FROM NMR DATA (40, 80, 120, 160, 250 MS NOESY EXPERIMENTS) AND DELTA DIHEDRAL ANGLES DERIVED FROM SIMULATION OF COSY CROSS PEAK PATTERNS. THE EIGHT DISTANCE RESTRAINED STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 2.0 PS OF THE DYNAMICS DURING DISTANCE RESTRAINED DYNAMICS AND MINIMIZED. THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE EIGHT FINAL STRUCTURES ARE: BOND (ANG): MDL1 MDL2 MDL3 MDL4 MDL5 MDL6 MDL7 MDL8 0.009 0.009 0.009 0.008 0.009 0.009 0.009 0.009 ANGLE (DEG): MDL1 MDL2 MDL3 MDL4 MDL5 MDL6 MDL7 MDL8 2.627 2.630 2.631 2.636 2.621 2.638 2.664 2.652 IMPROPER(DEG): MDL1 MDL2 MDL3 MDL4 MDL5 MDL6 MDL7 MDL8 0.866 0.850 0.808 0.874 0.841 0.803 0.881 0.808
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 8 / Conformers submitted total number: 8

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