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- PDB-3ce5: A bimolecular parallel-stranded human telomeric quadruplex in com... -

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Basic information

Entry
Database: PDB / ID: 3ce5
TitleA bimolecular parallel-stranded human telomeric quadruplex in complex with a 3,6,9-trisubstituted acridine molecule BRACO19
ComponentsDNA (5'-D(*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')
KeywordsDNA / bimolecular / parallel / human / telomere / quadruplex / complex / trisubstituted / acridine / BRACO19
Function / homologyChem-BRA / : / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCampbell, N.H. / Parkinson, G.N. / Reszka, A.P. / Neidle, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Structural basis of DNA quadruplex recognition by an acridine drug.
Authors: Campbell, N.H. / Parkinson, G.N. / Reszka, A.P. / Neidle, S.
History
DepositionFeb 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 11, 2017Group: Other
Revision 1.3Aug 30, 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_ref_seq / 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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: DNA (5'-D(*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')
B: DNA (5'-D(*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2195
Polymers7,5472
Non-polymers6723
Water97354
1
A: DNA (5'-D(*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')
B: DNA (5'-D(*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)16,43810
Polymers15,0944
Non-polymers1,3446
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-9 kcal/mol
Surface area4640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.338, 70.338, 34.293
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
DetailsThe second part of the biologically relevant assembly is generated by the operation: -x+1/2, -y+1/2, z+1/2

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Components

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


Mass: 3773.462 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This quadruplex-forming sequence occurs naturally in the telomeric ends of human chromosomes
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-BRA / 9-[4-(n,n-dimethylamino)phenylamino]-3,6-bis(3-pyrrolidinopropionamido) acridine / N,N'-(9-{[4-(dimethylamino)phenyl]amino}acridine-3,6-diyl)bis(3-pyrrolidin-1-ylpropanamide)


Mass: 593.762 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H43N7O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 mM DNA, 1.6 mM BRACO19, 200 mM ammonium sulphate, 20 mM sodium chloride, 20 mM potassium chloride, 20 mM lithium sulphate and 36 mM potassium cacodylate buffer at pH 6.5 equilibrated ...Details: 1.6 mM DNA, 1.6 mM BRACO19, 200 mM ammonium sulphate, 20 mM sodium chloride, 20 mM potassium chloride, 20 mM lithium sulphate and 36 mM potassium cacodylate buffer at pH 6.5 equilibrated against 1.6 M ammonium sulphate , VAPOR DIFFUSION, HANGING DROP, temperature 285.15K
Components of the solutions
IDNameCrystal-IDSol-ID
1200 mM ammonium sulphate11
2sodium chloride11
3potassium chloride11
4lithium sulphate11
5potassium cacodylate11
6BRACO19, the ligand under code BRA11
71.6 M ammonium sulphate12

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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: Jan 15, 2008 / 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: 2.5→35.17 Å / Num. all: 3003 / Num. obs: 2994 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 2.9 % / Biso Wilson estimate: 58.2 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 9.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / Num. unique all: 291 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1K8P

1k8p


Resolution: 2.5→35.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.965 / SU B: 7.026 / SU ML: 0.16 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.55 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21341 140 4.7 %RANDOM
Rwork0.18298 ---
all0.18446 2992 --
obs0.18446 2852 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.482 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å20 Å2
2--2.08 Å20 Å2
3----4.15 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 502 46 54 602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021617
X-RAY DIFFRACTIONr_angle_refined_deg2.8132.994948
X-RAY DIFFRACTIONr_chiral_restr0.1150.295
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02307
X-RAY DIFFRACTIONr_nbd_refined0.3060.2186
X-RAY DIFFRACTIONr_nbtor_refined0.3420.2335
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.236
X-RAY DIFFRACTIONr_metal_ion_refined0.1620.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.22
X-RAY DIFFRACTIONr_scbond_it2.8453683
X-RAY DIFFRACTIONr_scangle_it3.8644.5947
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 12 -
Rwork0.268 199 -
obs-199 100 %

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