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- PDB-1unm: Crystal structure of 7-Aminoactinomycin D with non-complementary DNA -

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Basic information

Entry
Database: PDB / ID: 1unm
TitleCrystal structure of 7-Aminoactinomycin D with non-complementary DNA
Components
  • 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
  • 7-AMINOACTINOMYCIN D
KeywordsDNA/ANTIBIOTIC / ACTINOMYCIN D / ACTINOMYCIN / ANTIBIOTIC / ANTI CANCER / CHROMOPHORE / DEPSIPEPTIDE / FLUORESCENT AGENT / ANTI TUMOR / NON-COMPLEMENTARY DNA / HOOGSTEN BASE-PAIR / DNA-ANTIBIOTIC COMPLEX
Function / homology7-AminoActinomycin / : / DNA
Function and homology information
Biological speciesSTREPTOMYCES ANTIBIOTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsAlexopoulos, E.C. / Klement, R. / Jares-Erijman, E.A. / Uson, I. / Jovin, T.M. / Sheldrick, G.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Crystal and Solution Structures of 7-Amino-Actinomycin D Complexes with D(Ttagbrut), D(Ttagtt) and D(Tttagttt)
Authors: Alexopoulos, E.C. / Jares-Erijman, E.A. / Jovin, T.M. / Klement, R. / Machinek, R. / Sheldrick, G.M. / Uson, I.
History
DepositionSep 11, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Jul 20, 2011Group: Other / Structure summary
Revision 1.3Nov 30, 2012Group: Other
Revision 1.4May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_polymer_linkage / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5May 22, 2019Group: Data collection / Refinement description / Category: pdbx_seq_map_depositor_info / refine
Item: _pdbx_seq_map_depositor_info.one_letter_code_mod / _refine.pdbx_ls_cross_valid_method
Revision 1.6Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.7Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
B: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
C: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
D: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
E: 7-AMINOACTINOMYCIN D
F: 7-AMINOACTINOMYCIN D


Theoretical massNumber of molelcules
Total (without water)10,0656
Polymers10,0656
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.586, 70.975, 39.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 1879.096 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein/peptide 7-AMINOACTINOMYCIN D / 7-Aminoactinomycin D


Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1274.462 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PX1) THE CHROMOPHORE PX1 IS A MODIFIED PXZ WITH C-NH2 REPLACING C-H IN POSITION 7 OF THE PHENOXAZONE RING.
Source: (synth.) STREPTOMYCES ANTIBIOTICUS (bacteria) / References: NOR: NOR00228, 7-AminoActinomycin
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
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) GROUP: 1 NAME: ACTINOMYCIN D CHAIN: E, F COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 11 DESCRIPTION: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PX1) THE CHROMOPHORE PX1 IS A MODIFIED PXZ WITH C-NH2 REPLACING C-H IN POSITION 7 OF THE PHENOXAZONE RING.

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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: 1.79 Å3/Da / Density % sol: 45 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6 / Details: (NH4)2SO4, NAK TART, NA CIT, PH 5.6, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.5418,0.8110
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.8111
ReflectionResolution: 2→20 Å / Num. obs: 10296 / % possible obs: 99.6 % / Redundancy: 1.83 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 11.87
Reflection shellResolution: 2→2.1 Å / Redundancy: 1.86 % / Rmerge(I) obs: 0.0896 / Mean I/σ(I) obs: 8.71 / % possible all: 98.8

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Num. parameters: 2356 / Num. restraintsaints: 2493 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2809 257 5 %IN THIN SHELLS
obs0.2431 -99.6 %-
all-4870 --
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 583.29
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms182 390 0 13 585
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.205
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.004
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.005
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.082
X-RAY DIFFRACTIONs_approx_iso_adps

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