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- PDB-3ey0: A new form of DNA-drug interaction in the minor groove of a coile... -

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Basic information

Entry
Database: PDB / ID: 3ey0
TitleA new form of DNA-drug interaction in the minor groove of a coiled coil
Components5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DT)-3'
KeywordsDNA / DNA drug pentamidine coiled-coil all-AT
Function / homology1,5-BIS(4-AMIDINOPHENOXY)PENTANE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsPous, J. / Moreno, T. / Subirana, J.A. / Campos, J.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Coiled-coil conformation of a pentamidine-DNA complex
Authors: Moreno, T. / Pous, J. / Subirana, J.A. / Campos, J.L.
History
DepositionOct 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 27, 2023Group: 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DT)-3'
B: 5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DT)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4494
Polymers6,0842
Non-polymers3652
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-8.5 kcal/mol
Surface area4410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.789, 27.789, 311.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsDouble stranded ATATATATAT

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Components

#1: DNA chain 5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DT)-3'


Mass: 3042.041 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized by using phosphoramiditine method
#2: Chemical ChemComp-PNT / 1,5-BIS(4-AMIDINOPHENOXY)PENTANE


Mass: 340.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24N4O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 278.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 mM MgCl2, 50 mM MES, 15% Isopropanol, 3.62 mM ds-DNA, 16.86 mM PNT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278.15K
Components of the solutions
IDNameCrystal-IDSol-ID
1MgCl211
2MES11
3Isopropanol11
4ds-DNA11
5PNT11
6MgCl212
7MES12
8Isopropanol12
9PNT12

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Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 24, 2008 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.52→50 Å / Num. all: 2899 / Num. obs: 2899 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 15.8 % / Biso Wilson estimate: 56.01 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 37.625
Reflection shellResolution: 2.52→2.56 Å / Redundancy: 18.4 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 15.75 / Num. unique all: 128 / Rsym value: 0.212 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.4.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: standard watson-crick DNA

Resolution: 2.52→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.885 / SU B: 25.145 / SU ML: 0.238 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.52 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27715 262 9.4 %RANDOM
Rwork0.21572 ---
obs0.22193 2511 93.62 %-
all-2782 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.499 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.52→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 26 51 481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021480
X-RAY DIFFRACTIONr_bond_other_d0.0030.02236
X-RAY DIFFRACTIONr_angle_refined_deg1.6443727
X-RAY DIFFRACTIONr_angle_other_deg1.2243571
X-RAY DIFFRACTIONr_chiral_restr0.0520.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02238
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0258
X-RAY DIFFRACTIONr_scbond_it1.0283200
X-RAY DIFFRACTIONr_scangle_it1.5774.5311
LS refinement shellResolution: 2.52→2.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 16 -
Rwork0.248 162 -
obs--95.19 %
Refinement TLS params.Method: refined / Origin x: 16.2235 Å / Origin y: 10.8519 Å / Origin z: 90.3531 Å
111213212223313233
T-0.0827 Å20.0185 Å20.007 Å2-0.1452 Å20.0225 Å2---0.0839 Å2
L5.9764 °20.6693 °2-3.1111 °2-1.5319 °2-0.8875 °2--3.9536 °2
S-0.3623 Å °0.3347 Å °0.045 Å °-0.0277 Å °0.1994 Å °-0.1417 Å °0.2706 Å °0.028 Å °0.1629 Å °

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