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- PDB-3t5e: Crystal structure of an intramolecular human telomeric DNA G-quad... -

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Basic information

Entry
Database: PDB / ID: 3t5e
TitleCrystal structure of an intramolecular human telomeric DNA G-quadruplex bound by the naphthalene diimide BMSG-SH-4
Componentshuman telomeric DNA sequence
KeywordsDNA / G-quadruplex / intramolecular / ligand-complex / telomeric
Function / homology: / Chem-T5E / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCollie, G.W. / Promontorio, R. / Parkinson, G.N.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Structural basis for telomeric g-quadruplex targeting by naphthalene diimide ligands.
Authors: Collie, G.W. / Promontorio, R. / Hampel, S.M. / Micco, M. / Neidle, S. / Parkinson, G.N.
History
DepositionJul 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: human telomeric DNA sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0145
Polymers6,9831
Non-polymers1,0314
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.034, 63.034, 42.389
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-26-

K

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Components

#1: DNA chain human telomeric DNA sequence


Mass: 6983.497 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DNA sequence synthesised by standard phosphoramidite chemistry
#2: Chemical ChemComp-T5E / 2,7-bis[4-(4-methylpiperazin-1-yl)butyl]-4,9-bis{[4-(4-methylpiperazin-1-yl)butyl]amino}benzo[lmn][3,8]phenanthroline-1 ,3,6,8(2H,7H)-tetrone / BMSG-SH2


Mass: 913.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H80N12O4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.48 Å3/Da / Density % sol: 64.67 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG400, 300 mM KBr, 50 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2011
RadiationMonochromator: Si III channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.94→54.59 Å / Num. all: 7197 / Num. obs: 7197 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 42.15 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.2
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2 / Num. unique all: 531 / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KF1

1kf1


Resolution: 2.1→10.2 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.672 / SU ML: 0.134 / Isotropic thermal model: Isotropic plus TLS / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28158 262 4.7 %RANDOM
Rwork0.24286 ---
all0.24474 5372 --
obs0.24474 5372 100 %-
Displacement parametersBiso mean: 40.688 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 465 69 38 572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021597
X-RAY DIFFRACTIONr_angle_refined_deg1.6222.999914
X-RAY DIFFRACTIONr_chiral_restr0.0550.287
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02272
X-RAY DIFFRACTIONr_scbond_it1.4653597
X-RAY DIFFRACTIONr_scangle_it2.3594.5914
LS refinement shellResolution: 2.1→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 15 -
Rwork0.385 373 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0016-0.00060.00010.0002-0.00010-0.4401-0.59310.94880.27090.24110.0693-0.7166-0.5570.19890.1236000.123600.1236-32.0347.3756-4.6732
20.0383-0.087-0.62110.19791.412210.0792-0.0118-0.30850.11880.31770.0804-0.15560.08240.2819-0.06850.1108-0.0017-0.00130.11220.00320.1354-26.06531.01551.5139
31.1106-3.09830.06718.6439-0.18720.00410.01520.2214-0.2858-0.24460.0211-0.61450.3820.5307-0.03640.1983-0.0062-0.00140.2132-0.00090.1955-17.7297-5.6219-11.1316
42.21290.86730.47960.5016-0.86016.8960.08080.32440.0534-0.4719-0.0705-0.0607-0.16960.0329-0.01030.1063-0.0068-0.00040.10760.00170.1394-28.64974.6698-17.9263
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 4
2X-RAY DIFFRACTION2A5 - 9
3X-RAY DIFFRACTION3A10 - 13
4X-RAY DIFFRACTION4A14 - 22

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