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- PDB-1xvn: echinomycin (ACGTACGT)2 complex -

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Basic information

Entry
Database: PDB / ID: 1xvn
Titleechinomycin (ACGTACGT)2 complex
Components
  • 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'
  • ECHINOMYCIN
KeywordsDNA/ANTIBIOTIC / BISINTERCALATOR / HOOGSTEEN BASEPAIR / DEPSIPEPTIDE / QUINOXALINE / THIOACETAL / ANTIBIOTIC / ANTITUMOR / DNA-ANTIBIOTIC COMPLEX
Function / homologyEchinomycin / 2-CARBOXYQUINOXALINE / : / DNA
Function and homology information
Biological speciesSTREPTOMYCES ECHINATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.5 Å
AuthorsCuesta-Seijo, J.A. / Sheldrick, G.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structures of Complexes between Echinomycin and Duplex DNA.
Authors: Cuesta-Seijo, J.A. / Sheldrick, G.M.
History
DepositionOct 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Mar 26, 2025Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_polymer_linkage / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'
B: ECHINOMYCIN
B: 2-CARBOXYQUINOXALINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6085
Polymers3,2362
Non-polymers3733
Water73941
1
A: 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'
B: ECHINOMYCIN
hetero molecules

A: 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'
B: ECHINOMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,21610
Polymers6,4714
Non-polymers7456
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area740 Å2
ΔGint-6.2 kcal/mol
Surface area3910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.928, 39.928, 80.098
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-21-

MG

21A-2007-

HOH

31A-2009-

HOH

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Components

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


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein/peptide ECHINOMYCIN / QUINOMYCIN A


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 809.008 Da / Num. of mol.: 1 / 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-QUI / 2-CARBOXYQUINOXALINE


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 174.156 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
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.
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.32 %
Crystal growpH: 6
Details: PEG 200, PEG 3350, MGCL2, MES, SPERMINE-HCL, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 20011
2PEG 335011
3MgCl211
4MES11
5spermine-HCl11
6H2O11
7PEG 20012
8PEG 335012
9MgCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 11, 2003
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→26.2 Å / Num. obs: 6499 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 21.27 % / Rmerge(I) obs: 0.0424 / Rsym value: 0.0424 / Net I/σ(I): 39.11
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 20.44 % / Rmerge(I) obs: 0.4225 / Mean I/σ(I) obs: 9.03 / Rsym value: 0.4225 / % possible all: 98.4

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Processing

Software
NameClassification
EPMRphasing
SHELXL-97refinement
HKL-2000data reduction
XDSdata scaling
RefinementMethod to determine structure: molecular replacement / Resolution: 1.5→26.2 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THE SKELETON OF ECHINOMYCIN IS NEARLY SYMMETRIC (NOT MODELLED TO DO SO), THE BRIDGE IS NOT. BOTH POSSIBLE ORIENTATIONS OF BINDING WERE OBSERVED AND ARE MODELLED AS DISORDERED/MICROHETE.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 571 -RANDOM
all0.202 6499 --
obs0.202 -99 %-
Refine analyzeNum. disordered residues: 7
Refinement stepCycle: LAST / Resolution: 1.5→26.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms66 161 25 41 293

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