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- PDB-3nz7: A bimolecular anti-parallel-stranded Oxytricha nova telomeric qua... -

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Basic information

Entry
Database: PDB / ID: 3nz7
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 / FLUORINATION
Function / homology: / Chem-SNS / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 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 16, 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
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-12 kcal/mol
Surface area3500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.574, 42.704, 26.995
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
11B-61-

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 telomere 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-SNS / 3,6-bis(3-(3'-(S)-fluoropyrrolindino)propionamido)acridine / N,N'-acridine-3,6-diylbis{3-[(3S)-3-fluoropyrrolidin-1-yl]propanamide}


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


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: The 4 ul drop contained 0.75 mM quadruplex DNA, 0.75 mM ligand, 10 % MPD, 12.5 mM magnesium chloride, 12.5 mM spermine.4HCl and 10 mM potassium cacodylate buffer at pH 6.5. This was ...Details: The 4 ul drop contained 0.75 mM quadruplex DNA, 0.75 mM ligand, 10 % MPD, 12.5 mM magnesium chloride, 12.5 mM spermine.4HCl and 10 mM potassium cacodylate buffer at pH 6.5. This was equilibrated against a reservoir well solution of 600 ul of 30% 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: Feb 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9702 Å / Relative weight: 1
ReflectionResolution: 1.1→7.952 Å / Num. all: 25994 / Num. obs: 25994 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 25.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.1-1.1650.0876.81885137920.08798.8
1.16-1.239.10.0995.93338236640.099100
1.23-1.31110.0757.73755734130.075100
1.31-1.4211.10.077.73557432140.07100
1.42-1.5611.10.0687.73273729610.068100
1.56-1.7411.10.0657.12992727040.065100
1.74-2.0110.90.0767.32605623930.076100
2.01-2.4610.10.0787.42069620530.07899.6
2.46-3.487.80.061101074713710.06185.1
3.48-7.9616.20.0621026404290.06243.3

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1l1h


Resolution: 1.1→7.805 Å / Occupancy max: 1 / Occupancy min: 0.42 / SU ML: 0.11 / σ(F): 0.19 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1592 1286 4.97 %Random
Rwork0.1379 ---
obs0.1389 25901 96.95 %-
all-25901 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.83 Å2 / ksol: 0.526 e/Å3
Displacement parametersBiso max: 39.48 Å2 / Biso mean: 11.9351 Å2 / Biso min: 3.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.3432 Å2-0 Å20 Å2
2---1.5357 Å2-0 Å2
3---0.1926 Å2
Refinement stepCycle: LAST / Resolution: 1.1→7.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 506 40 188 734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015609
X-RAY DIFFRACTIONf_angle_d1.96937
X-RAY DIFFRACTIONf_chiral_restr0.09894
X-RAY DIFFRACTIONf_plane_restr0.02627
X-RAY DIFFRACTIONf_dihedral_angle_d34.658265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.1-1.14390.13711420.116526792821268397
1.1439-1.19580.14551520.1035274728992747100
1.1958-1.25860.11431400.0979279629362796100
1.2586-1.33710.13181620.1068277529372775100
1.3371-1.43980.15771430.1184279229352792100
1.4398-1.58360.14611560.1249281129672811100
1.5836-1.81020.13011510.1142281429652818100
1.8102-2.27130.15591280.1353287029982870100
2.2713-7.80560.21371120.194323312443233178

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