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- PDB-1pfe: Echinomycin-(gcgtacgc)2 complex -

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Basic information

Entry
Database: PDB / ID: 1pfe
TitleEchinomycin-(gcgtacgc)2 complex
Components
  • 5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-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: 1.1 Å
AuthorsCuesta-Seijo, J.A.
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
DepositionMay 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: 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 1.5Apr 3, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_validate_polymer_linkage / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _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_comp_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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_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

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Assembly

Deposited unit
A: 5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3'
B: ECHINOMYCIN
B: 2-CARBOXYQUINOXALINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6205
Polymers3,2372
Non-polymers3843
Water1,44180
1
A: 5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3'
B: ECHINOMYCIN
hetero molecules

A: 5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3'
B: ECHINOMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,24110
Polymers6,4734
Non-polymers7686
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area730 Å2
ΔGint-6.4 kcal/mol
Surface area3960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.374, 39.374, 79.734
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-2002-

HOH

21A-2013-

HOH

31A-2019-

HOH

41A-2024-

HOH

DetailsThe second part of the biological assembly is generated by: -x, -x+y, -z

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Components

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


Mass: 2427.605 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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.: 80 / 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.

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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: 3.51 Å3/Da / Density % sol: 64.98 %
Crystal growpH: 4.5
Details: LI2SO4, MGCL2, METHANOL, NAAC, SPERMINE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Li2SO411
2MgCl211
3Methanol11
4NaAc11
5Spermine11
6H2O11
7MgCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8162
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 19, 2002
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8162 Å / Relative weight: 1
ReflectionResolution: 1.1→21 Å / Num. obs: 15164 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 14.91 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 30.01
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 13.05 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 11.48 / % possible all: 95.7

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Processing

Software
NameClassification
EPMRphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TROSTIN A - (GCGTACGC)2 COMPLEX

Resolution: 1.1→21 Å / Num. parameters: 2979 / Num. restraintsaints: 2074 / Cross valid method: FREE R / σ(F): 0
StereochEM target val spec case: TARGETS FOR ECHINOMYCIN BUILT FROM THE CSD
Stereochemistry target values: STANDARD SHELX FOR THE DNA, ENGH & HUBER FOR THE STANDARD PROTEIN PARTS OF ECHINOMYCIN, BUILT FROM THE CSD FOR THE REST
Details: THE SKELETON OF ECHINOMYCIN IS NEARLY SYMMETRIC (NOT MODELLED TO DO SO), THE BRIDGE IS NOT. BOTH POSSIBLE ORIENTATIONS OF BINDING WERE OBSERVED, BUT SKELETON POSITIONS NEARLY OVERLAP, SO ...Details: THE SKELETON OF ECHINOMYCIN IS NEARLY SYMMETRIC (NOT MODELLED TO DO SO), THE BRIDGE IS NOT. BOTH POSSIBLE ORIENTATIONS OF BINDING WERE OBSERVED, BUT SKELETON POSITIONS NEARLY OVERLAP, SO ONLY THE BRIDGE WAS MODELLED AS DISORDERED/MICROHETEROGENEITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.168 478 3 %THIN SHELLS
all0.146 15164 --
obs0.146 -97.2 %-
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 149 / Occupancy sum non hydrogen: 303
Refinement stepCycle: LAST / Resolution: 1.1→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms66 161 25 80 332
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d0.036
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.172
X-RAY DIFFRACTIONs_zero_chiral_vol0.068
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.041
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
LS refinement shellResolution: 1.1→1.2 Å / % reflection obs: 95.7 %

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