+Open data
-Basic information
Entry | Database: PDB / ID: 1a7y | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF ACTINOMYCIN D | ||||||||||||
Components | ACTINOMYCIN D | ||||||||||||
Keywords | ANTIBIOTIC / ACTINOMYCIN / ANTITUMOR / ANTICANCER / CHROMOPHORE / DEPSIPEPTIDE | ||||||||||||
Function / homology | Actinomycin D / ETHYL ACETATE / METHANOL / : Function and homology information | ||||||||||||
Biological species | STREPTOMYCES ANTIBIOTICUS (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / AB INITIO / Resolution: 0.94 Å | ||||||||||||
Authors | Schafer, M. / Sheldrick, G.M. / Bahner, I. / Lackner, H. | ||||||||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 1998 Title: Crystal Structures of Actinomycin D and Actinomycin Z3. Authors: Schafer, M. / Sheldrick, G.M. / Bahner, I. / Lackner, H. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1a7y.cif.gz | 25.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1a7y.ent.gz | 18.6 KB | Display | PDB format |
PDBx/mmJSON format | 1a7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a7y_validation.pdf.gz | 430.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1a7y_full_validation.pdf.gz | 431.9 KB | Display | |
Data in XML | 1a7y_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 1a7y_validation.cif.gz | 4.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/1a7y ftp://data.pdbj.org/pub/pdb/validation_reports/a7/1a7y | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein/peptide | Type: Polypeptide / Class: Antibiotic / Mass: 1291.446 Da / Num. of mol.: 3 / Source method: isolated from a natural source Details: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ) Source: (natural) STREPTOMYCES ANTIBIOTICUS (bacteria) / References: NOR: NOR00228, Actinomycin D #2: Chemical | ChemComp-EEE / #3: Chemical | ChemComp-MOH / | Compound details | ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS ...ACTINOMYCI | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.5 Å3/Da / Density % sol: 18 % |
---|---|
Crystal grow | pH: 5 / Details: PH 5.0 |
Crystal grow | *PLUS Method: unknown |
Components of the solutions | *PLUS Common name: ethyl acetate/methanol |
-Data collection
Diffraction | Mean temperature: 133 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Nov 3, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 0.94→999 Å / Num. obs: 14126 / % possible obs: 95.1 % / Redundancy: 4.38 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 0.94→1.05 Å / Redundancy: 2.85 % / Rmerge(I) obs: 0.072 / Mean I/σ(I) obs: 11.9 / % possible all: 90.5 |
Reflection | *PLUS Num. measured all: 95014 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: AB INITIO / Highest resolution: 0.94 Å / Num. parameters: 2875 / Num. restraintsaints: 3689 / Cross valid method: FREE R / σ(F): 0 StereochEM target val spec case: NO RESTRAINTS ON DISTANCES AND ANGLES Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.039
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 318 / Occupancy sum non hydrogen: 314 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 0.94 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.575 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|