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- PDB-5ytz: Crystal structure of echinomycin-d(ACGTCGT)2 complex -

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Basic information

Entry
Database: PDB / ID: 5ytz
TitleCrystal structure of echinomycin-d(ACGTCGT)2 complex
Components
  • DNA (5'-D(P*AP*CP*GP*TP*CP*GP*(UD))-3')
  • Echinomycin
KeywordsANTIBIOTIC/DNA / Echinomycin / DNA intercalator / antibiotic / Echinomycin-DNA complex / mismatched base pairs / T-T mismatch / pyrimidine-pyrimidine base pairing / DNA mismatch repair (MMR) / non-canonical duplex structure / 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: 1.55 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.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.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*TP*CP*GP*(UD))-3')
B: DNA (5'-D(P*AP*CP*GP*TP*CP*GP*(UD))-3')
D: Echinomycin
F: Echinomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,82011
Polymers5,9754
Non-polymers8467
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint14 kcal/mol
Surface area2470 Å2
Unit cell
Length a, b, c (Å)41.759, 41.759, 138.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-101-

MN

21B-101-

MN

31D-103-

K

41A-210-

HOH

51A-221-

HOH

61B-205-

HOH

71B-236-

HOH

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Components

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DNA chain / Protein/peptide , 2 types, 4 molecules ABDF

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


Mass: 2178.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#2: 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, 107 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: 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
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.33 Å3/Da / Density % sol: 52.86 %
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 500 ul of 30% MPD reservoir solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.92014 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92014 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 16665 / % possible obs: 99.9 % / Redundancy: 17.3 % / Biso Wilson estimate: 9.93 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 12.9
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.141 / Num. unique obs: 908 / Rsym value: 0.141 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHASER7.0.005phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3go3

3go3


Resolution: 1.55→27.16 Å / SU ML: 0.139 / Cross valid method: FREE R-VALUE / σ(F): 1.383 / Phase error: 24.757
RfactorNum. reflection% reflection
Rfree0.235 1649 9.895 %
Rwork0.206 --
obs0.209 16665 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.55 Å2
Refinement stepCycle: LAST / Resolution: 1.55→27.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms106 286 51 100 543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008482
X-RAY DIFFRACTIONf_angle_d1.344680
X-RAY DIFFRACTIONf_dihedral_angle_d34.649178
X-RAY DIFFRACTIONf_chiral_restr0.07968
X-RAY DIFFRACTIONf_plane_restr0.00730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5517-1.59740.27141200.24711112X-RAY DIFFRACTION87
1.5974-1.64890.28861360.23321220X-RAY DIFFRACTION95
1.6489-1.70780.23481410.21111240X-RAY DIFFRACTION100
1.7078-1.77620.25181310.24271281X-RAY DIFFRACTION100
1.7762-1.8570.23071440.20951270X-RAY DIFFRACTION100
1.857-1.95490.2521480.21661260X-RAY DIFFRACTION100
1.9549-2.07740.22981430.21361280X-RAY DIFFRACTION100
2.0774-2.23770.21861340.21281264X-RAY DIFFRACTION100
2.2377-2.46270.26441370.21181283X-RAY DIFFRACTION100
2.4627-2.81880.25131390.20781270X-RAY DIFFRACTION100
2.8188-3.55010.22221360.18471260X-RAY DIFFRACTION99
3.5501-27.16350.21391400.18841276X-RAY DIFFRACTION100

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