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- PDB-2adw: Crystal structure of Echinomycin-(ACGTACGT)2 solved by SAD -

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Basic information

Entry
Database: PDB / ID: 2adw
TitleCrystal structure of Echinomycin-(ACGTACGT)2 solved by SAD
Components
  • 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'
  • ECHINOMYCIN
KeywordsDNA/ANTIBIOTIC / DNA-ANTIBIOTIC COMPLEX / BISINTERCALATOR / HOOGSTEEN BASEPAIR / DEPSIPEPTIDE / QUINOXALINE / THIOACETAL / ANTIBIOTIC / ANTITUMOR
Function / homologyEchinomycin / NICKEL (II) ION / 2-CARBOXYQUINOXALINE / : / DNA
Function and homology information
Biological speciesSTREPTOMYCES ECHINATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.6 Å
AuthorsCuesta-Seijo, J.A. / Sheldrick, G.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Serendipitous Sad Phasing of an Echinomycin-(Acgtacgt)2 Bisintercalation Complex.
Authors: Cuesta-Seijo, J.A. / Weiss, M.S. / Sheldrick, G.M.
History
DepositionJul 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: 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 1.5Sep 9, 2020Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: pdbx_struct_conn_angle / pdbx_validate_polymer_linkage ...pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / struct / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.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.value / _struct.title / _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'
C: 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'
E: 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'
G: 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'
H: ECHINOMYCIN
I: ECHINOMYCIN
J: ECHINOMYCIN
K: ECHINOMYCIN
H: 2-CARBOXYQUINOXALINE
I: 2-CARBOXYQUINOXALINE
J: 2-CARBOXYQUINOXALINE
K: 2-CARBOXYQUINOXALINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,65519
Polymers12,9438
Non-polymers1,71311
Water1,54986
1
E: 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'
G: 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'
J: ECHINOMYCIN
K: ECHINOMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,29210
Polymers6,4714
Non-polymers8216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-5.7 kcal/mol
Surface area4280 Å2
MethodPISA
2
A: 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'
C: 5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'
H: ECHINOMYCIN
I: ECHINOMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3639
Polymers6,4714
Non-polymers8925
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-3.9 kcal/mol
Surface area3940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.904, 80.904, 48.194
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11E-2014-

HOH

21E-2028-

HOH

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Components

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DNA chain / Protein/peptide , 2 types, 8 molecules ACEGHIJK

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


Mass: 2426.617 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein/peptide
ECHINOMYCIN / QUINOMYCIN A


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 809.008 Da / Num. of mol.: 4 / 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 , 5 types, 97 molecules HIJK

#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-QUI / 2-CARBOXYQUINOXALINE


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 174.156 Da / Num. of mol.: 8 / 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.: 86 / 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: 2.6 Å3/Da / Density % sol: 51.6 %
Crystal growpH: 6
Details: PEG 200, PEG3350, MES, SPERMINE, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 20011
2PEG335011
3MES11
4spermine11
5H2O11
6PEG 20012
7PEG335012
8MES12
9H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 12, 2003 / Details: DOUBLE CRYSTAL MONOCHROMATOR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 21134 / % possible obs: 97.6 % / Observed criterion σ(I): -99 / Redundancy: 12.42 % / Rmerge(I) obs: 0.0716 / Net I/σ(I): 18.7
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 10.07 % / Rmerge(I) obs: 0.3941 / Mean I/σ(I) obs: 5.33 / % possible all: 96.3

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Processing

Software
NameClassification
SHELXDphasing
SHELXEmodel building
SHELXL-97refinement
HKL-2000data reduction
XDSdata scaling
RefinementMethod to determine structure: AB INITIO / Resolution: 1.6→30 Å / Cross valid method: FREE R / σ(F): -99 / Stereochemistry target values: ENGH & HUBER. PARKINSON / Details: CGLS SHELX REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2103 -RANDOM
all0.18 21134 --
obs0.18 -97.6 %-
Refine analyzeNum. disordered residues: 17
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms250 644 110 86 1090

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