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- PDB-6gim: Structure of the DNA duplex d(AAATTT)2 with [N-(3-chloro-4-((4,5-... -

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Basic information

Entry
Database: PDB / ID: 6gim
TitleStructure of the DNA duplex d(AAATTT)2 with [N-(3-chloro-4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)-4-((4,5-dihydro-1H-imidazol-2- yl)amino)benzamide] - (drug JNI18)
ComponentsDNA (5'-D(*AP*AP*AP*TP*TP*T)-3')
KeywordsDNA / AT-rich DNA / DNA binding drugs / Minor groove binding drugs / antiparasitic drugs / Trypanosoma brucei
Function / homologyChem-EZK / DNA
Function and homology information
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsMillan, C.R. / Dardonvile, C. / de Koning, H.P. / Saperas, N. / Campos, J.L.
Funding support Spain, United Kingdom, 4items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessSAF2015-66690-R Spain
Spanish Ministry of Economy and CompetitivenessBFU2009-10380 Spain
Spanish Ministry of Economy and CompetitivenessFPU12/04824, EST14/00449 Spain
Wellcome Trust085349 United Kingdom
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
DepositionMay 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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)8,50210
Polymers7,2294
Non-polymers1,2736
Water1,71195
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)4,4144
Polymers3,6142
Non-polymers8002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPISA
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)4,4636
Polymers3,6142
Non-polymers8484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
MethodPISA
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)4,0635
Polymers3,6142
Non-polymers4483
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)22.630, 40.470, 72.255
Angle α, β, γ (deg.)90.00, 93.91, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11D-101-

EZK

21C-101-

EZK

31C-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.) Trypanosoma brucei (eukaryote)
#2: Chemical ChemComp-EZK / [4-[(3-chloranyl-4-imidazolidin-2-ylideneazaniumyl-phenyl)carbamoyl]phenyl]-imidazolidin-2-ylidene-azanium


Mass: 399.877 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H22ClN7O
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.304846 Å3/Da / Density meas: 0.127 Mg/m3 / Density % sol: 46.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10 mM magnesium acetate, 0.1 mM spermine, 5% 2-methyl-2,4-pentanediol (MPD); equilibrated against 20% MPD reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.43→36.04 Å / Num. obs: 12256 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 12.7 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.033 / Rrim(I) all: 0.081 / Χ2: 0.92 / Net I/av σ(I): 13.4 / Net I/σ(I): 2.79
Reflection shellResolution: 1.43→7.81 Å / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 602 / CC1/2: 0.858 / Rpim(I) all: 0.376 / Rrim(I) all: 0.642 / Χ2: 0.72 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
iMOSFLM7.2.2data reduction
Aimless0.6.3data scaling
MOLREP11.4.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Idealised DNA model from TURBO

Resolution: 1.43→36.04 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.476 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.068 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19286 557 4.7 %RANDOM
Rwork0.14342 ---
obs0.14585 11306 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.164 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20.71 Å2
2---0.63 Å20 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.43→36.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 480 87 96 663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.011629
X-RAY DIFFRACTIONr_bond_other_d0.0060.02340
X-RAY DIFFRACTIONr_angle_refined_deg1.9371.391946
X-RAY DIFFRACTIONr_angle_other_deg1.6822.749790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.681012
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.02426
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02138
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_it2.2281.543629
X-RAY DIFFRACTIONr_scbond_other2.2271.542630
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7512.334947
X-RAY DIFFRACTIONr_long_range_B_refined3.0714.202856
X-RAY DIFFRACTIONr_long_range_B_other2.9113.735839
X-RAY DIFFRACTIONr_rigid_bond_restr3.4973968
X-RAY DIFFRACTIONr_sphericity_free15.162570
X-RAY DIFFRACTIONr_sphericity_bonded8.7465933
LS refinement shellResolution: 1.426→1.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 37 -
Rwork0.171 810 -
obs--93.9 %

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