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- PDB-3go3: Interactions of an echinomycin-DNA complex with manganese(II) ions -

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Basic information

Entry
Database: PDB / ID: 3go3
TitleInteractions of an echinomycin-DNA complex with manganese(II) ions
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 / : / DI(HYDROXYETHYL)ETHER / 2-CARBOXYQUINOXALINE / : / DNA
Function and homology information
Biological speciesSTREPTOMYCES ECHINATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsPfoh, R. / Cuesta-Seijo, J.A. / Sheldrick, G.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Interaction of an Echinomycin-DNA Complex with Manganese Ion
Authors: Pfoh, R. / Cuesta-Seijo, J.A. / Sheldrick, G.M.
History
DepositionMar 18, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: 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_struct_conn_angle / 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 / _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.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.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 / _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: 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'
C: ECHINOMYCIN
D: ECHINOMYCIN
C: 2-CARBOXYQUINOXALINE
D: 2-CARBOXYQUINOXALINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,38411
Polymers6,4714
Non-polymers9137
Water81145
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-11.2 kcal/mol
Surface area4010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.544, 26.544, 162.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2004-

HOH

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Components

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

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


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


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, 52 molecules CD

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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.
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: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growpH: 6
Details: 24% V/V PEG 200, 6% W/V PEG 3350, 16MM MANGANESE(II) CHLORIDE, 20MM SPERMINE TETRACHLORIDE, 0.1M MES BUFFER (PH 6.0), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 20011
2PEG 350011
3manganese(II) chloride11
4spermine tetrachloride11
5MES11
6H2O11
7PEG 20012
8PEG 350012
9manganese(II) chloride12
10spermine tetrachloride12
11MES12
12H2O12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineTypeIDWavelength
SYNCHROTRONSLS X10SA11
ROTATING ANODEMACSCIENCE21.54178
ROTATING ANODEMACSCIENCE31.54178
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDMay 23, 2008
MAR scanner 345 mm plate2IMAGE PLATEDec 23, 2004
BRUKER SMART 60003CCDDec 21, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI 111 DOUBLE CRYSTALSINGLE WAVELENGTHMx-ray1
2MULTI- LAYERSINGLE WAVELENGTHMx-ray1
3MULTI-LAYERSADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.541781
ReflectionResolution: 1.1→30 Å / Num. obs: 23140 / % possible obs: 92.2 % / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.0328 / Net I/σ(I): 24.06
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 2.17 % / Rmerge(I) obs: 0.2019 / Mean I/σ(I) obs: 4.44 / % possible all: 76.5

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Processing

Software
NameClassification
SHELXDphasing
SHELXL-97refinement
XDSdata reduction
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.1→20 Å / Num. parameters: 4945 / Num. restraintsaints: 6976 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH & 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, 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/MICROHETE
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1177 5.25 %RANDOM
all0.163 22400 --
obs0.162 -94.3 %-
Solvent computationSolvent model: BABINET
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms134 322 57 45 558
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.229
X-RAY DIFFRACTIONs_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.055
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.041
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.05
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.065
X-RAY DIFFRACTIONs_approx_iso_adps0.077

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