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- PDB-2et0: The structure of a three-way DNA junction in complex with a metal... -

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Basic information

Entry
Database: PDB / ID: 2et0
TitleThe structure of a three-way DNA junction in complex with a metallo-supramolecular helicate reveals a new target for drugs
Components5'-D(*CP*GP*TP*AP*CP*G)-3'
KeywordsDNA / Drug-DNA complex / 3-way junction / DNA structure recognition
Function / homology: / Chem-NPM / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsOleksi, A. / Blanco, A.G. / Boer, R. / Uson, I. / Aymami, J. / Coll, M.
CitationJournal: ANGEW.CHEM.INT.ED.ENGL. / Year: 2006
Title: Molecular Recognition of a Three-Way DNA Junction by a Metallosupramolecular Helicate
Authors: Oleksi, A. / Blanco, A.G. / Boer, R. / Uson, I. / Aymami, J. / Rodger, A. / Hannon, M.J. / Coll, M.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The het group NPM 1, 2, 3 exists as a complex of three molecules of NPM with two FE(II) ...HETEROGEN The het group NPM 1, 2, 3 exists as a complex of three molecules of NPM with two FE(II) molecules in the structure. The IUPAC name for the complete ligand is 'tris (1,1-bis(N-(4-phenyl)-2-pyridylcaboxaldimine) methane) bis-iron(II) tetrachloride

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*GP*TP*AP*CP*G)-3'
B: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,83613
Polymers3,6182
Non-polymers2,21711
Water81145
1
A: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules

A: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules

A: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,61527
Polymers5,4283
Non-polymers5,18824
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
2
B: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules

B: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules

B: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,89212
Polymers5,4283
Non-polymers1,4649
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)71.200, 71.200, 71.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-6-

FE2

21A-7-

FE2

31B-9-

FE2

DetailsThe asymmetric unit contains one-third of the 3-way junction, the 2nd and 3rd part are generated by the cube body diagonal 3-fold axis. For residues 10 to 16, the biological assembly is constructed by applying symops z,x,y and y,z,x

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Components

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


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-NPM / N-[(1E)-PYRIDIN-2-YLMETHYLENE]-N-[4-(4-{[(1E)-PYRIDIN-2-YLMETHYLENE]AMINO}BENZYL)PHENYL]AMINE / 1,1-BIS(N-(4-PHENYL)-2-PYRIDYLCARBOXALDIMINE)METHANE


Mass: 376.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C25H20N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.08M Mg acetate, 0.05M TrisCl, pH 8.5, 5% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
10.08M Mg acetate11
20.05M TrisCl11
35% PEG40011
40.08M Mg acetate12
50.05M TrisCl12
65% PEG40012

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1611.739, 1.749, 1.627
SYNCHROTRONESRF ID14-220.933
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDSep 18, 2003mirrors
ADSC QUANTUM 42CCDDec 5, 2003mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1two Si(111) crystalsMADMx-ray1
2Diamond (111), Ge(220)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.7391
21.7491
31.6271
40.9331
ReflectionResolution: 1.7→22.8 Å / Num. all: 7149 / Num. obs: 7149 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 50 % / Rmerge(I) obs: 0.0537 / Net I/σ(I): 29.1
Reflection shellHighest resolution: 1.7 Å / % possible all: 97.8

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Processing

Software
NameClassification
ProDCdata collection
XDSdata reduction
SHELXDEphasing
SHELXL-97refinement
XDSdata scaling
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.7→22.5 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.291 325 random
Rwork0.256 --
all0.26 7149 -
obs0.258 6182 -
Displacement parametersBiso mean: 23.45 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 239 151 45 435
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_from_restr_planes0.041
X-RAY DIFFRACTIONs_similar_dist0.055
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.008
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.025

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