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- PDB-3sc8: Crystal structure of an intramolecular human telomeric DNA G-quad... -

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Basic information

Entry
Database: PDB / ID: 3sc8
TitleCrystal structure of an intramolecular human telomeric DNA G-quadruplex bound by the naphthalene diimide BMSG-SH-3
ComponentsHuman telomeric repeat sequence
KeywordsDNA / G-quadruplex / intramolecular / ligand-complex / telomeric
Function / homology: / Chem-R8G / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 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
DepositionJun 7, 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
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_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

Downloads & links

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Assembly

Deposited unit
A: Human telomeric repeat sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9585
Polymers6,9831
Non-polymers9744
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.870, 50.870, 52.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-26-

K

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Components

#1: DNA chain Human telomeric repeat sequence


Mass: 6983.497 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DNA sequence synthesized by standard by phosphoramidite chemistry
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-R8G / 2,7-bis[3-(4-methylpiperazin-1-yl)propyl]-4,9-bis{[3-(4-methylpiperazin-1-yl)propyl]amino}benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone


Mass: 857.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H72N12O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 56.16 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 % PEG400, 50 mM potassium chloride, 20 mM potassium cacodylate, 50 mM sodium cacodylate, 100 mM lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.17→26.23 Å / Num. all: 4385 / Num. obs: 4385 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Biso Wilson estimate: 58.898 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 32.1
Reflection shellResolution: 2.17→2.23 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.5 / Num. unique all: 324 / % 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: 2.302→10.3 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.573 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28828 161 4.4 %RANDOM
Rwork0.25839 ---
all0.25989 3467 --
obs0.25989 3467 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: 45.257 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.302→10.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 447 65 29 541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021572
X-RAY DIFFRACTIONr_angle_refined_deg1.0483877
X-RAY DIFFRACTIONr_chiral_restr0.060.284
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02261
X-RAY DIFFRACTIONr_scbond_it1.8313572
X-RAY DIFFRACTIONr_scangle_it2.8844.5877
LS refinement shellResolution: 2.302→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.481 11 -
Rwork0.404 240 -
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)
18.95910.59221.63086.32171.34465.7714-0.2620.21230.9019-0.8007-0.09970.4667-0.4757-0.43140.36170.17060.1202-0.08410.352-0.11920.2173-19.028-14.74-0.902
214.06171.27529.72212.26531.818.336-0.0325-0.32-0.6067-0.19610.02520.00230.0784-0.3380.00730.070.02290.04550.1199-0.05430.1663-19.39-21.812-0.652
30.0432-0.45070.54484.9221-6.081410.9385-0.10250.01220.02450.9255-0.3739-0.20770.05510.58060.47650.66130.10350.06490.29940.01610.1999-10.09-23.35711.863
47.6711-0.68153.999710.249910.485413.7216-0.52420.62590.18710.17250.792-0.3823-0.35381.3182-0.26780.4831-0.2113-0.02570.355-0.03040.212-5.678-7.88110.338
520.37925.285910.53183.84414.1868.9480.0168-0.22290.85820.5714-0.1345-0.2014-0.5280.39720.11770.4706-0.1351-0.02760.2512-0.01240.2004-7.774-7.9223.48
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 5
2X-RAY DIFFRACTION2A6 - 9
3X-RAY DIFFRACTION3A10 - 14
4X-RAY DIFFRACTION4A15 - 18
5X-RAY DIFFRACTION5A19 - 22

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