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- PDB-5yty: Crystal structure of echinomycin-d(ACGACGT/ACGTCGT) complex -

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Basic information

Entry
Database: PDB / ID: 5yty
TitleCrystal structure of echinomycin-d(ACGACGT/ACGTCGT) complex
Components
  • DNA (5'-D(P*AP*CP*GP*AP*CP*GP*T)-3')
  • DNA (5'-D(P*AP*CP*GP*TP*CP*GP*T)-3')
  • echinomycin
KeywordsANTIBIOTIC/DNA / DNA intercalator / Echinomycin-DNA complex / Watson-Crick / heptamer duplex / ANTIBIOTIC-DNA complex
Function / homologyEchinomycin / : / 2-CARBOXYQUINOXALINE / : / DNA
Function and homology information
Biological speciesStreptomyces echinatus (bacteria)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsHou, M.H. / Wu, P.C. / Kao, Y.F.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex
Authors: Wu, P.C. / Tzeng, S.L. / Chang, C.K. / Kao, Y.F. / Waring, M.J. / Hou, M.H.
History
DepositionNov 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Structure summary
Category: pdbx_entry_details / pdbx_molecule_features / struct_ref
Item: _struct_ref.db_name / _struct_ref.pdbx_db_accession
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_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.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(P*AP*CP*GP*AP*CP*GP*T)-3')
B: DNA (5'-D(P*AP*CP*GP*TP*CP*GP*T)-3')
D: echinomycin
F: echinomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,65411
Polymers5,8544
Non-polymers8007
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint2 kcal/mol
Surface area2470 Å2
Unit cell
Length a, b, c (Å)46.362, 46.362, 48.005
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-226-

HOH

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Components

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DNA chain , 2 types, 2 molecules AB

#1: DNA chain DNA (5'-D(P*AP*CP*GP*AP*CP*GP*T)-3')


Mass: 2122.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#2: DNA chain DNA (5'-D(P*AP*CP*GP*TP*CP*GP*T)-3')


Mass: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

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Protein/peptide , 1 types, 2 molecules DF

#3: Protein/peptide echinomycin


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 809.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ...Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
Source: (natural) Streptomyces echinatus (bacteria) / References: NOR: NOR01126, Echinomycin

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Non-polymers , 4 types, 72 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Chemical
ChemComp-QUI / 2-CARBOXYQUINOXALINE


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 174.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H6N2O2
Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ...Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
References: Echinomycin
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. ...THE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, ECHINOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND TWO LIGANDS (HET) QUI.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20mM MES (pH 6.0), 10mM MgCl2, 2mM spermine 4HCl, 2% 2-methyl-2,4-pentanediol (MPD), 10mM MnSO4 and 10mM KBr by equilibrating against 500ul of 30% MPD reservoir solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→30 Å / Num. obs: 12609 / % possible obs: 99.5 % / Redundancy: 6 % / Biso Wilson estimate: 10.94 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 17.4
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.141 / Num. unique obs: 816 / Rsym value: 0.141 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXmodel building
PHASER7.0.005phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YTZ

5ytz


Resolution: 1.58→20.6 Å / SU ML: 0.207 / Cross valid method: FREE R-VALUE / σ(F): 1.389 / Phase error: 29.675
RfactorNum. reflection% reflection
Rfree0.263 1246 9.882 %
Rwork0.222 --
obs0.226 12609 79.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.51 Å2
Refinement stepCycle: LAST / Resolution: 1.58→20.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms106 287 51 65 509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01484
X-RAY DIFFRACTIONf_angle_d1.475687
X-RAY DIFFRACTIONf_dihedral_angle_d28.635150
X-RAY DIFFRACTIONf_chiral_restr0.10476
X-RAY DIFFRACTIONf_plane_restr0.01430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5815-1.64480.2311810.1994632X-RAY DIFFRACTION40
1.6448-1.71970.2216930.2375855X-RAY DIFFRACTION53
1.7197-1.81030.31271080.29741082X-RAY DIFFRACTION69
1.8103-1.92360.34881360.28561235X-RAY DIFFRACTION78
1.9236-2.0720.3691510.25531438X-RAY DIFFRACTION91
2.072-2.28030.32581730.26651535X-RAY DIFFRACTION97
2.2803-2.60970.27391710.21551534X-RAY DIFFRACTION98
2.6097-3.28580.31781620.21451545X-RAY DIFFRACTION97
3.2858-20.60360.17291710.1751507X-RAY DIFFRACTION95

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