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- PDB-3eum: A bimolecular anti-parallel-stranded Oxytricha nova telomeric qua... -

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Basic information

Entry
Database: PDB / ID: 3eum
TitleA bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine BSU-6066
Components5'-D(*DGP*DGP*DGP*DGP*DTP*DTP*DTP*DTP*DGP*DGP*DGP*DG)-3'
KeywordsDNA / quadruplex / Oxtyricha nova / BSU-6066 / BSU6066 / anti-parallel / bimolecular / macromolecule / G-quadruplex
Function / homology: / 3,6-Bis[3-(azepan-1-yl)propionamido]acridine / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsCampbell, N.H. / Parkinson, G. / Neidle, S.
CitationJournal: Biochemistry / Year: 2009
Title: Selectivity in Ligand Recognition of G-Quadruplex Loops.
Authors: Campbell, N.H. / Patel, M. / Tofa, A.B. / Ghosh, R. / Parkinson, G.N. / Neidle, S.
History
DepositionOct 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Sep 6, 2023Group: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,2837
Polymers7,6112
Non-polymers6725
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-9.4 kcal/mol
Surface area3650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.620, 42.307, 27.079
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: DNA chain 5'-D(*DGP*DGP*DGP*DGP*DTP*DTP*DTP*DTP*DGP*DGP*DGP*DG)-3'


Mass: 3805.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The sequence occurs naturally in Oxytricha nova
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NCQ / 3,6-Bis[3-(azepan-1-yl)propionamido]acridine / N,N'-acridine-3,6-diylbis(3-azepan-1-ylpropanamide)


Mass: 515.690 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H41N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2 microliter drops containing 5% v/v MPD, 0.50 mM DNA, 0.25 mM Ligand, 40 mM Potassium chloride, 5 mM Magnesium chloride, 4.1 Spermine equilibrated against 35% v/v MPD, pH 7.0, VAPOR ...Details: 2 microliter drops containing 5% v/v MPD, 0.50 mM DNA, 0.25 mM Ligand, 40 mM Potassium chloride, 5 mM Magnesium chloride, 4.1 Spermine equilibrated against 35% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285.15K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Potassium chloride11
3Magnesium chloride11
4Spermine11
5MPD12

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.540562 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Aug 9, 2007 / Details: Oxford diffraction Nova
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.540562 Å / Relative weight: 1
ReflectionResolution: 1.78→24.35 Å / Num. all: 6576 / Num. obs: 5372 / % possible obs: 81.7 % / Redundancy: 2.3 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.57
Reflection shellResolution: 1.78→1.93 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.28 / Num. unique all: 539 / % possible all: 39.1

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Processing

Software
NameVersionClassification
CrysalisProdata collection
PHASERphasing
REFMAC5.2.0019refinement
CrysalisProdata reduction
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1L1H

1l1h


Resolution: 1.78→24.35 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.901 / SU B: 3.508 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27042 238 4.5 %RANDOM
Rwork0.22174 ---
obs0.2241 5106 81.91 %-
all-5372 --
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: 16.544 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2---0.93 Å20 Å2
3---1.8 Å2
Refinement stepCycle: LAST / Resolution: 1.78→24.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 506 42 52 600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021610
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8943936
X-RAY DIFFRACTIONr_angle_other_deg
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_restr0.0660.294
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02298
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.340.2211
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.2346
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0820.210
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.216
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2720.29
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_scbond_it1.4383683
X-RAY DIFFRACTIONr_scangle_it2.0554.5936
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 9 -
Rwork0.313 107 -
obs--24.79 %

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