+Open data
-Basic information
Entry | Database: PDB / ID: 1xvk | ||||||
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Title | X-ray structure of an Echinomycin-(GCGTACGC)2 complex | ||||||
Components |
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Keywords | DNA/ANTIBIOTIC / BISINTERCALATOR / HOOGSTEEN BASEPAIR / DEPSIPEPTIDE / QUINOXALINE / THIOACETAL / ANTIBIOTIC / ANTITUMOR / DNA-ANTIBIOTIC COMPLEX | ||||||
Function / homology | Echinomycin / 2-CARBOXYQUINOXALINE / : / DNA Function and homology information | ||||||
Biological species | STREPTOMYCES ECHINATUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.26 Å | ||||||
Authors | Cuesta-Seijo, J.A. / Sheldrick, G.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structures of Complexes between Echinomycin and Duplex DNA. Authors: Cuesta-Seijo, J.A. / Sheldrick, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xvk.cif.gz | 28.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xvk.ent.gz | 21.1 KB | Display | PDB format |
PDBx/mmJSON format | 1xvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xvk_validation.pdf.gz | 420.4 KB | Display | wwPDB validaton report |
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Full document | 1xvk_full_validation.pdf.gz | 424.3 KB | Display | |
Data in XML | 1xvk_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 1xvk_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/1xvk ftp://data.pdbj.org/pub/pdb/validation_reports/xv/1xvk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 2427.605 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
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#2: Protein/peptide | 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 / | ||||
#4: Chemical | 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 / | Compound details | THE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. ...THE ECHINOMYCI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.36 % |
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Crystal grow | pH: 4.5 Details: PEG550MME, MGCL2, NAAC, SPERMINE- HCL, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 11, 2003 |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→26 Å / Num. obs: 10337 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 15.87 % / Rmerge(I) obs: 0.0495 / Rsym value: 0.0495 / Net I/σ(I): 28.25 |
Reflection shell | Resolution: 1.26→1.4 Å / Redundancy: 9.78 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 6.7 / Rsym value: 0.35 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement / Resolution: 1.26→26 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.
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Refine analyze | Num. disordered residues: 9 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.26→26 Å
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