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- PDB-5lit: Structure of the DNA duplex d(AAATTT)2 with the potential antipar... -

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Basic information

Entry
Database: PDB / ID: 5lit
TitleStructure of the DNA duplex d(AAATTT)2 with the potential antiparasitic drug 6XV at 1.25 A resolution
ComponentsDNA (5'-D(*AP*AP*AP*TP*TP*T)-3')
KeywordsDNA / All AT DNA / Antiparasitic Drug / Minor Groove Binding Drug
Function / homologyChem-6XV / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsMillan, C.R. / Dardonville, C. / de Koning, H.P. / Saperas, N. / Lourdes Campos, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Government of Catalonia2015 SGR 080 Spain
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Functional and structural analysis of AT-specific minor groove binders that disrupt DNA-protein interactions and cause disintegration of the Trypanosoma brucei kinetoplast.
Authors: Millan, C.R. / Acosta-Reyes, F.J. / Lagartera, L. / Ebiloma, G.U. / Lemgruber, L. / Nue Martinez, J.J. / Saperas, N. / Dardonville, C. / de Koning, H.P. / Campos, J.L.
History
DepositionJul 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Structure summary / Category: audit_author / citation / citation_author / Item: _citation.title
Revision 1.2Jun 28, 2017Group: Database references / Structure summary / Category: audit_author / citation_author / struct
Item: _audit_author.name / _audit_author.pdbx_ordinal ..._audit_author.name / _audit_author.pdbx_ordinal / _citation_author.name / _struct.title
Revision 1.3Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5May 8, 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 / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _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_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _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_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (5'-D(*AP*AP*AP*TP*TP*T)-3')
C: DNA (5'-D(*AP*AP*AP*TP*TP*T)-3')
A: DNA (5'-D(*AP*AP*AP*TP*TP*T)-3')
B: DNA (5'-D(*AP*AP*AP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,41611
Polymers7,2294
Non-polymers1,1877
Water2,972165
1
D: DNA (5'-D(*AP*AP*AP*TP*TP*T)-3')
hetero molecules

D: DNA (5'-D(*AP*AP*AP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3906
Polymers3,6142
Non-polymers7754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
C: DNA (5'-D(*AP*AP*AP*TP*TP*T)-3')
hetero molecules

C: DNA (5'-D(*AP*AP*AP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3906
Polymers3,6142
Non-polymers7754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y,-z-11
3
A: DNA (5'-D(*AP*AP*AP*TP*TP*T)-3')
B: DNA (5'-D(*AP*AP*AP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0275
Polymers3,6142
Non-polymers4123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)22.330, 40.250, 72.423
Angle α, β, γ (deg.)90.00, 93.67, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11C-102-

MG

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Components

#1: DNA chain
DNA (5'-D(*AP*AP*AP*TP*TP*T)-3')


Mass: 1807.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-6XV / 4-((4,5-dihydro-1H-imidazol-2-yl)amino)-N-(4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)benzamide dihydrochloride


Mass: 363.416 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H21N7O
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 277.1 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10 mM Magnesium Acetate / PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9787 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.247→36.14 Å / Num. obs: 16801 / % possible obs: 92.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 5.519 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.1
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 5.5 / CC1/2: 0.965 / % possible all: 89.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLM7.2.1data reduction
Aimless0.5.25data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AAATTT

Resolution: 1.25→36.14 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.28 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16688 853 5.1 %RANDOM
Rwork0.12053 ---
obs0.12284 15741 92.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.883 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.45 Å2
2---0.04 Å2-0 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.25→36.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 480 85 165 730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.013626
X-RAY DIFFRACTIONr_bond_other_d0.0060.02337
X-RAY DIFFRACTIONr_angle_refined_deg2.5181.524940
X-RAY DIFFRACTIONr_angle_other_deg1.8943784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1220.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0380.02373
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02127
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4571.019626
X-RAY DIFFRACTIONr_scbond_other1.4561.019627
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7041.54941
X-RAY DIFFRACTIONr_long_range_B_refined2.38211.5591032
X-RAY DIFFRACTIONr_long_range_B_other1.82410.395911
X-RAY DIFFRACTIONr_rigid_bond_restr13.643962
X-RAY DIFFRACTIONr_sphericity_free20.239521
X-RAY DIFFRACTIONr_sphericity_bonded6.76851046
LS refinement shellResolution: 1.247→1.279 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 63 -
Rwork0.141 1122 -
obs--90.67 %

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