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- PDB-316d: Selectivity of F8-actinomycin D for RNA:DNA hybrids and its anti-... -

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Basic information

Entry
Database: PDB / ID: 316d
TitleSelectivity of F8-actinomycin D for RNA:DNA hybrids and its anti-leukemia activity
Components
  • 8-FLUORO-ACTINOMYCIN D
  • DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
KeywordsDNA/ANTIBIOTIC / ACTINOMYCIN D / ACTINOMYCIN / F8-ACTINOMYCIN / ANTI CANCER / ANTITUMOR / CHROMOPHORE / DEPSIPEPTIDE / DNA-ANTIBIOTIC COMPLEX / ANTIBIOTIC
Function / homology8-Fluoro-Actinomycin D / : / DNA
Function and homology information
Biological speciesSTREPTOMYCES ANTIBIOTICUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTakusagawa, F. / Takusagawa, K.T. / Carlson, R.G. / Weaver, R.F.
CitationJournal: Bioorg.Med.Chem. / Year: 1997
Title: Selectivity of F8-Actinomycin D for RNA:DNA Hybrids and its Anti-Leukemia Activity.
Authors: Takusagawa, F. / Takusagawa, K.T. / Carlson, R.G. / Weaver, R.F.
History
DepositionMar 5, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Nov 5, 1997Provider: 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 25, 2018Group: Advisory / Data collection / Structure summary / Category: chem_comp / pdbx_validate_polymer_linkage / Item: _chem_comp.pdbx_synonyms
Revision 1.6Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
B: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
C: 8-FLUORO-ACTINOMYCIN D


Theoretical massNumber of molelcules
Total (without water)6,1633
Polymers6,1633
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.770, 62.770, 43.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein/peptide 8-FLUORO-ACTINOMYCIN D / DACTINOMYCIN


Type: Polypeptide / Class: Antibiotic / Mass: 1309.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXF) THE CHROMOPHORE PXF IS A MODIFIED PXZ WITH C-F REPLACING C-H IN POSITION 8 OF THE PHENOXAZONE RING.
Source: (natural) STREPTOMYCES ANTIBIOTICUS (bacteria) / References: NOR: NOR00228, 8-Fluoro-Actinomycin D
Compound detailsACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS ...ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS REPRESENTED BY THE SEQUENCE (SEQRES)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.04 Å3/Da / Density % sol: 75.6 %
Crystal growpH: 7
Details: PH 7.00, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 299.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4CACODYLATE11
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 26 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.0 mMoligonucleotide1drop
210 mM1dropMgCl2
320 mMcacodylate/HCl1drop
41.5 mMF8AMD1drop
515 %MPD1reservoir
61
71

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Data collection

DiffractionMean temperature: 299 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 1, 1995
RadiationMonochromator: GRAPHITE 002 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→7 Å / Num. obs: 1839 / % possible obs: 95 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.075 / Rsym value: 0.075
Reflection shellResolution: 3→3.2 Å / Rmerge(I) obs: 0.0018 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.0018 / % possible all: 90
Reflection
*PLUS
% possible obs: 95 %
Reflection shell
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.002

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
ELMSdata reduction
KUAVSTdata scaling
KUMDSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DDH051

Resolution: 3→7 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.261 184 10 %
Rwork0.212 --
obs0.212 1839 95 %
Displacement parametersBiso mean: 38 Å2
Refine Biso Class: ALL ATOMS / Details: TR / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms91 322 0 0 413
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3→3.2 Å / Total num. of bins used: 1 /
Rfactor% reflection
Rfree0.261 10 %
obs-100 %
Software
*PLUS
Name: 'X-PLOR' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24

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