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

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Basic information

Entry
Database: PDB / ID: 3eui
TitleA bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine BSU-6042 in a large unit cell
Components5'-D(*DGP*DGP*DGP*DGP*DTP*DTP*DTP*DTP*DGP*DGP*DGP*DG)-3'
KeywordsDNA / quadruplex / Oxytricha nova / BSU-6042 / BSU6042 / anti-parallel / bimolecular / macromolecule / G-quadruplex
Function / homology: / Chem-NC5 / Chem-NCI / SPERMINE / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Sep 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'
C: 5'-D(*DGP*DGP*DGP*DGP*DTP*DTP*DTP*DTP*DGP*DGP*DGP*DG)-3'
D: 5'-D(*DGP*DGP*DGP*DGP*DTP*DTP*DTP*DTP*DGP*DGP*DGP*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,82415
Polymers15,2224
Non-polymers1,60311
Water2,918162
1
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)8,5138
Polymers7,6112
Non-polymers9026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-10.1 kcal/mol
Surface area3490 Å2
MethodPISA
2
C: 5'-D(*DGP*DGP*DGP*DGP*DTP*DTP*DTP*DTP*DGP*DGP*DGP*DG)-3'
D: 5'-D(*DGP*DGP*DGP*DGP*DTP*DTP*DTP*DTP*DGP*DGP*DGP*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3117
Polymers7,6112
Non-polymers7005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-10.1 kcal/mol
Surface area3990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.356, 42.542, 48.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains two biological units.

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Components

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DNA chain , 1 types, 4 molecules ABCD

#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.: 4 / Source method: obtained synthetically / Details: This sequence occurs naturally in Oxytricha nova

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Non-polymers , 5 types, 173 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NC5 / 3-[(2R)-2-ethylpiperidin-1-yl]-N-[6-({3-[(2S)-2-ethylpiperidin-1-yl]propanoyl}amino)acridin-3-yl]propanamide


Mass: 543.743 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H45N5O2
#4: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#5: Chemical ChemComp-NCI / 3,6-Bis{3-[(2R)-(2-ethylpiperidino)]propionamido}acridine / N,N'-acridine-3,6-diylbis{3-[(2R)-2-ethylpiperidin-1-yl]propanamide}


Mass: 543.743 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H45N5O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.88 Å3/Da / Density % sol: 34.61 %
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 20, 2006 / Details: mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→27.72 Å / Num. all: 6193 / Num. obs: 5854 / % possible obs: 94.5 % / Observed criterion σ(I): 3 / Redundancy: 3.61 % / Biso Wilson estimate: 34.254 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.59 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 5.2 / Num. unique all: 545 / % possible all: 92.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L1H

1l1h


Resolution: 2.2→27.68 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.406 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.878 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28506 277 4.7 %RANDOM
Rwork0.23422 ---
obs0.23691 5575 94.51 %-
all-5854 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.772 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---3.27 Å20 Å2
3---3.63 Å2
Refinement stepCycle: LAST / Resolution: 2.2→27.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1012 102 162 1276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211237
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1531892
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_restr0.0750.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02612
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.340.2506
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2694
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.140.230
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.217
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_it1.81731381
X-RAY DIFFRACTIONr_scangle_it2.2194.51892
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 22 -
Rwork0.231 389 -
obs--91.74 %

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