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

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Basic information

Entry
Database: PDB / ID: 3nyp
TitleA bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine ligand containing bis-3-fluoropyrrolidine end side chains
Components5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
KeywordsDNA / QUADRUPLEX / OXTYRICHA NOVA / BSU-6039 / BSU6039 / ANTI-PARALLEL / BIMOLECULAR / MACROMOLECULE / G-QUADRUPLEX / TELOMERE / ACRIDINE
Function / homology: / Chem-RNR / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.179 Å
AuthorsCampbell, N.H. / Neidle, S.
CitationJournal: Org.Biomol.Chem. / Year: 2011
Title: Fluorine in medicinal chemistry: beta-fluorination of peripheral pyrrolidines attached to acridine ligands affects their interactions with G-quadruplex DNA.
Authors: Campbell, N.H. / Smith, D.L. / Reszka, A.P. / Neidle, S. / O'Hagan, D.
History
DepositionJul 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
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 / 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_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.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.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.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

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
B: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2637
Polymers7,6112
Non-polymers6525
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-15 kcal/mol
Surface area3990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.800, 44.460, 28.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-147-

HOH

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Components

#1: DNA chain 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'


Mass: 3805.460 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This telomeric sequence occurs naturally in the organism 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-RNR / 3,6-bis(3-(3'-(R)-fluoropyrrolindino)propionamido)acridine / N,N'-acridine-3,6-diylbis{3-[(3R)-3-fluoropyrrolidin-1-yl]propanamide}


Mass: 495.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31F2N5O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: The 5 Ul drop contained 1.2 mM quadruplex DNA, 1.2 mM ligand, 4% MPD, 4 mM potassium chloride, 4 mM magnesium chloride, 4 mM sodium chloride, 4 mM lithium sulphate, 3.2 mM spermine.4HCl and ...Details: The 5 Ul drop contained 1.2 mM quadruplex DNA, 1.2 mM ligand, 4% MPD, 4 mM potassium chloride, 4 mM magnesium chloride, 4 mM sodium chloride, 4 mM lithium sulphate, 3.2 mM spermine.4HCl and 16 mM potassium cacodylate buffer at pH 6.5. This was equilibrated against a reservoir well solution of 500 Ul of 45% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 285.15K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9702 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9702 Å / Relative weight: 1
ReflectionResolution: 1.18→21.99 Å / Num. all: 23982 / Num. obs: 23982 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.18-1.243.50.125.71199134230.1297.8
1.24-1.323.60.0897.41191932890.08998.5
1.32-1.413.60.0748.81139131360.07499.2
1.41-1.523.70.0797.71068029140.07999.3
1.52-1.673.70.0629.1993027200.06299.6
1.67-1.863.70.04910.6901924630.04999.3
1.86-2.153.60.04712.2788121860.04799.7
2.15-2.643.30.05410.5611418420.05498.3
2.64-3.733.40.03715.1480814010.03794.5
3.73-20.7482.80.03217.817146080.03268.3

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L1H

1l1h


Resolution: 1.179→21.99 Å / Occupancy max: 1 / Occupancy min: 0.42 / SU ML: 0.13 / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 1183 5.08 %Random
Rwork0.1647 ---
obs0.1658 23275 94.59 %-
all-23275 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.946 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso max: 56.09 Å2 / Biso mean: 14.8626 Å2 / Biso min: 4.94 Å2
Baniso -1Baniso -2Baniso -3
1-1.5525 Å20 Å2-0 Å2
2--1.2304 Å20 Å2
3----2.7829 Å2
Refinement stepCycle: LAST / Resolution: 1.179→21.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 506 40 177 723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.024609
X-RAY DIFFRACTIONf_angle_d2.125937
X-RAY DIFFRACTIONf_chiral_restr0.14194
X-RAY DIFFRACTIONf_plane_restr0.02227
X-RAY DIFFRACTIONf_dihedral_angle_d31.085265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.179-1.23270.28081400.198324402580244086
1.2327-1.29760.22581280.166325972725259790
1.2976-1.37890.19531420.153926732815267393
1.3789-1.48540.21131610.160227432904274395
1.4854-1.63480.1781510.157428112962281197
1.6348-1.87130.16671490.132928703019287098
1.8713-2.35720.17171610.151329053066290599
2.3572-21.99340.17161510.173130533204305398

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