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- PDB-1unj: Crystal structure of a 7-Aminoactinomycin D complex with non-comp... -

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Basic information

Entry
Database: PDB / ID: 1unj
TitleCrystal structure of a 7-Aminoactinomycin D complex with non-complementary DNA
Components
  • 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
  • 7-AMINO-ACTINOMYCIN D
KeywordsDNA/ANTIBIOTIC / ACTINOMYCIN D / ACTINOMYCIN / ANTIBIOTIC / ANTI CANCER / ANTITUMOR / CHROMOPHORE / DEPSIPEPTIDE / DNA-ANTIBIOTIC COMPLEX / FLUORESCENT AGENT / HOOGSTEN BASE-PAIR
Function / homology7-AminoActinomycin / : / DNA
Function and homology information
Biological speciesSTREPTOMYCES ANTIBIOTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 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 10, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 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 1.4Mar 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...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.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.6May 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 1.7Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.8Oct 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-AMINO-ACTINOMYCIN D
F: 7-AMINO-ACTINOMYCIN D
G: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
H: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
I: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
J: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
K: 7-AMINO-ACTINOMYCIN D
L: 7-AMINO-ACTINOMYCIN D
M: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
N: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
O: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
P: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
Q: 7-AMINO-ACTINOMYCIN D
R: 7-AMINO-ACTINOMYCIN D
S: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
T: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
U: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
V: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
W: 7-AMINO-ACTINOMYCIN D
X: 7-AMINO-ACTINOMYCIN D


Theoretical massNumber of molelcules
Total (without water)40,26124
Polymers40,26124
Non-polymers00
Water25214
1
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-AMINO-ACTINOMYCIN D
F: 7-AMINO-ACTINOMYCIN D
G: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
H: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
I: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
J: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
K: 7-AMINO-ACTINOMYCIN D
L: 7-AMINO-ACTINOMYCIN D


Theoretical massNumber of molelcules
Total (without water)20,13112
Polymers20,13112
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
N: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
O: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
P: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
Q: 7-AMINO-ACTINOMYCIN D
R: 7-AMINO-ACTINOMYCIN D
S: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
T: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
U: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
V: 5'-D(*TP*TP*AP*GP*BRU*TP)-3'
W: 7-AMINO-ACTINOMYCIN D
X: 7-AMINO-ACTINOMYCIN D


Theoretical massNumber of molelcules
Total (without water)20,13112
Polymers20,13112
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.222, 71.222, 108.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 1879.096 Da / Num. of mol.: 16 / Source method: obtained synthetically
#2: Protein/peptide
7-AMINO-ACTINOMYCIN D / DACTINOMYCIN / 7-Aminoactinomycin D


Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1274.462 Da / Num. of mol.: 8 / 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.: 14 / 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, K, L, Q, R, W, X 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: 1.97 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: NA.CITRATE PH 5.6, NA.ACETATE,(NH4)2SO4,HANGING DROP,T 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9050,0.9196,0.9204
DetectorType: MARRESEARCH / Date: Jul 15, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9051
20.91961
30.92041
ReflectionResolution: 2.5→20 Å / Num. obs: 11527 / % possible obs: 99 % / Redundancy: 10.15 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.57
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 9.37 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.27 / % possible all: 93.3

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / Num. parameters: 8996 / Num. restraintsaints: 17002 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.3163 577 5 %IN THIN SHELLS
obs0.276 -99 %-
all-11527 --
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2236.88
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms728 1503 0 14 2245
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.015
X-RAY DIFFRACTIONs_similar_dist0.029
X-RAY DIFFRACTIONs_from_restr_planes0.159
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.003
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.004
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.002
X-RAY DIFFRACTIONs_approx_iso_adps

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