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- PDB-1s45: Crystal structure analysis of the DNA quadruplex d(TGGGGT) S1 -

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Basic information

Entry
Database: PDB / ID: 1s45
TitleCrystal structure analysis of the DNA quadruplex d(TGGGGT) S1
Components5'-D(*TP*GP*GP*GP*GP*T)-3'
KeywordsDNA / QUADRUPLEX DNA / THYMINE TRIADS / THALLIUM
Function / homologyTHALLIUM (I) ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCaceres, C. / Wright, G. / Gouyette, C. / Parkinson, G. / Subirana, J.A.
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: A Thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+1/Na+1 ions
Authors: Caceres, C. / Wright, G. / Gouyette, C. / Parkinson, G. / Subirana, J.A.
History
DepositionJan 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*TP*GP*GP*GP*GP*T)-3'
B: 5'-D(*TP*GP*GP*GP*GP*T)-3'
C: 5'-D(*TP*GP*GP*GP*GP*T)-3'
D: 5'-D(*TP*GP*GP*GP*GP*T)-3'
E: 5'-D(*TP*GP*GP*GP*GP*T)-3'
F: 5'-D(*TP*GP*GP*GP*GP*T)-3'
G: 5'-D(*TP*GP*GP*GP*GP*T)-3'
H: 5'-D(*TP*GP*GP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,31616
Polymers15,0428
Non-polymers1,2748
Water2,018112
1
A: 5'-D(*TP*GP*GP*GP*GP*T)-3'
B: 5'-D(*TP*GP*GP*GP*GP*T)-3'
C: 5'-D(*TP*GP*GP*GP*GP*T)-3'
D: 5'-D(*TP*GP*GP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3639
Polymers7,5214
Non-polymers8425
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*TP*GP*GP*GP*GP*T)-3'
F: 5'-D(*TP*GP*GP*GP*GP*T)-3'
G: 5'-D(*TP*GP*GP*GP*GP*T)-3'
H: 5'-D(*TP*GP*GP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9537
Polymers7,5214
Non-polymers4323
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.259, 35.410, 32.057
Angle α, β, γ (deg.)83.73, 61.78, 76.68
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain
5'-D(*TP*GP*GP*GP*GP*T)-3'


Mass: 1880.251 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: This sequence occurs naturally in Tetrahymena
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Tl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.01 Å3/Da / Density % sol: 38.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, sodium cacodylate, magnesium chloride, spermine tetrahydrochlorhide, thallium acetate, lysine-anthraquinone, d(TGGGGT), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3magnesium chloride11
4spermine tetrahydrochlorhide11
5thallium acetate11
6lysine-anthraquinone11
7H2O11
8sodium cacodylate12
9magnesium chloride12
10thallium acetate12
11H2O12
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMsodium cacodylate1droppH6.5
230 mM1dropMgCl2
31 mMspermine 4HCl1drop
40.25 mMThallium acetate1drop
520000 nMlysine-anthraquinone1drop
60.5 mMd(TGGGGT)1drop
760 mM1reservoirMgCl2
810 %MPD1reservoir
91
101
111

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.917 / Wavelength: 0.9800, 0.9772, 0.9076
DetectorDetector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9171
20.981
30.97721
40.90761
ReflectionResolution: 2.2→20 Å / Num. obs: 5055 / Redundancy: 3.16 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.11 / Num. unique all: 455 / % possible all: 83.3
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 93.5 %
Reflection shell
*PLUS
% possible obs: 83.3 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ENTRY UDF036

Resolution: 2.2→18.5 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 279248.41 / Data cutoff high rms absF: 279248.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.239 503 10.7 %RANDOM
Rwork0.173 ---
all0.195 5055 --
obs0.173 4721 87.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.0896 Å2 / ksol: 0.370837 e/Å3
Displacement parametersBiso mean: 10.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20.52 Å2-1.96 Å2
2---4.5 Å20 Å2
3---4.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→18.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 966 8 112 1086
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.021.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it1.492
X-RAY DIFFRACTIONc_scangle_it1.952.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 63 10 %
Rwork0.24 567 -
obs--69.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA-RNA_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
% reflection Rfree: 9.3 % / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0039
X-RAY DIFFRACTIONc_angle_deg0.66
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01

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