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- PDB-146d: SOLUTION STRUCTURE OF THE MITHRAMYCIN DIMER-DNA COMPLEX -

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Entry
Database: PDB / ID: 146d
TitleSOLUTION STRUCTURE OF THE MITHRAMYCIN DIMER-DNA COMPLEX
ComponentsDNA (5'-D(*TP*CP*GP*CP*GP*A)-3')
KeywordsDNA / MITHRAMYCIN DIMER
Function / homologyChem-CRH / DNA
Function and homology information
MethodSOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION
AuthorsSastry, M. / Patel, D.J.
CitationJournal: Biochemistry / Year: 1993
Title: Solution structure of the mithramycin dimer-DNA complex.
Authors: Sastry, M. / Patel, D.J.
History
DepositionNov 9, 1993Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_name_sys / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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.name / _chem_comp.type / _entity_name_com.entity_id / _entity_name_sys.entity_id / _entity_name_sys.name / _pdbx_database_status.process_site / _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.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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 2.1Jan 19, 2022Group: Database references / Structure summary / Category: chem_comp / database_2 / entity_name_com
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_name_com.entity_id
Revision 2.2May 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 (5'-D(*TP*CP*GP*CP*GP*A)-3')
B: DNA (5'-D(*TP*CP*GP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8219
Polymers3,6182
Non-polymers2,2037
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)2 / 2all calculated structures submitted
Representative

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Components

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


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED
#2: Polysaccharide beta-D-Olivopyranose-(1-3)-beta-D-Olivopyranose


Type: oligosaccharide / Mass: 278.299 Da / Num. of mol.: 2
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 / 2,6-DIDEOXY-3 C-METHYL-D-RIBOPYRANOSIDE


Type: oligosaccharide / Mass: 422.468 Da / Num. of mol.: 2 / 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 / MAGNESIUM


Mass: 24.305 Da / Num. of mol.: 1 / 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 / 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.: 2 / Source method: obtained synthetically / Formula: C21H24O7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE HYDROXYL PROTONS IN THE RELAXATION MATRIX REFINED STRUCTURES ARE NOT WELL DETERMINED. THE HYDROPHILIC SIDE CHAIN, THE B SUGAR RESIDUE DDA 1 AND DDA 7, AND RESIDUES T 1 AND C 2 ARE UNDETERMINED.

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Version: 2.1 / Developer: Brunger / Classification: refinement
RefinementMethod: MOLECULAR DYNAMICS, MATRIX RELAXATION / Software ordinal: 1
Details: TWO STARTING MODELS WERE OBTAINED BY DOCKING THE MG2+ COORDINATED MITHRAMYCIN DIMER IN THE MINOR GROOVE OF A AND B FORM D(TCGCGA) DUPLEX. THESE MODELS WERE SUBSEQUENTLY REFINED BY DISTANCE ...Details: TWO STARTING MODELS WERE OBTAINED BY DOCKING THE MG2+ COORDINATED MITHRAMYCIN DIMER IN THE MINOR GROOVE OF A AND B FORM D(TCGCGA) DUPLEX. THESE MODELS WERE SUBSEQUENTLY REFINED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE NMR DATA. THE TWO DISTANCE-REFINED STRUCTURES WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE FINAL TWO STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 1 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND MINIMIZED. THE R VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE R FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE TWO FINAL STRUCTURES ARE: MODEL 1 MODEL 2 R FACTOR 0.146 0.136 BOND (ANGSTROMS) 0.016 0.013 ANGLES (DEGREES) 3.410 3.369. THE STRUCTURE EXHIBITS APPROXIMATE TWO-FOLD SYMMETRY, PERPENDICULAR TO THE HELICAL AXIS AND PASSING THROUGH THE MAGNESIUM IN THE COMPLEX. THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B OF MODEL 1 WHEN APPLIED TO CHAIN A OF MODEL 1. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B OF MODEL 2 WHEN APPLIED TO CHAIN A OF MODEL 2.
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 2 / Conformers submitted total number: 2

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