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- PDB-1s47: Crystal structure analysis of the DNA quadruplex d(TGGGGT)S2 -

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Basic information

Entry
Database: PDB / ID: 1s47
TitleCrystal structure analysis of the DNA quadruplex d(TGGGGT)S2
Components5'-D(*TP*GP*GP*GP*GP*T)-3'
KeywordsDNA / QUADRUPLEX DNA / THYMINE TRIADS AND TETRADS / THALLIUM
Function / homologyTHALLIUM (I) ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.3Aug 23, 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 / _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(*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'
I: 5'-D(*TP*GP*GP*GP*GP*T)-3'
J: 5'-D(*TP*GP*GP*GP*GP*T)-3'
K: 5'-D(*TP*GP*GP*GP*GP*T)-3'
L: 5'-D(*TP*GP*GP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,95025
Polymers22,56312
Non-polymers1,38713
Water1,54986
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)7,9768
Polymers7,5214
Non-polymers4554
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)7,8179
Polymers7,5214
Non-polymers2965
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: 5'-D(*TP*GP*GP*GP*GP*T)-3'
J: 5'-D(*TP*GP*GP*GP*GP*T)-3'
K: 5'-D(*TP*GP*GP*GP*GP*T)-3'
L: 5'-D(*TP*GP*GP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1578
Polymers7,5214
Non-polymers6364
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.319, 56.341, 51.746
Angle α, β, γ (deg.)90.00, 99.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 1880.251 Da / Num. of mol.: 12 / Source method: obtained synthetically / Details: This sequence occurs naturally in Tetrahymena.
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Tl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 38.46 %
Crystal growTemperature: 277 K / pH: 6.5
Details: PEG 400, sodium cacodylate, magnesium chloride, spermine, tetrahydrochlorhide, thallium acetate, lysine-anthraquinone, d(TGGGGT), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.50
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2sodium cacodylate11
3magnesium chloride11
4spermine11
5tetrahydrochlorhide11
6thallium acetate11
7lysine-anthraquinone11
8H2O11
9PEG 40012
10magnesium chloride12
11thallium acetate12
12sodium cacodylate12
13H2O12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / 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
72.5 %(v/v)PEG4001drop
825 %(v/v)PEG4001reservoir
91
101
111
121
131

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98
DetectorDetector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 10915 / Redundancy: 5.43 % / Biso Wilson estimate: 6.4 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.16 / % possible all: 97.3
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % possible obs: 98.3 % / Redundancy: 5.43 %
Reflection shell
*PLUS
% possible obs: 97.3 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S45

1s45


Resolution: 2.5→19.84 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 498502.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: FRIEDEL PAIRS ARE NOT MERGED IN THE NUMBER OF UNIQUE REFLECTIONS FOR DATA COLLECTION
RfactorNum. reflection% reflectionSelection details
Rfree0.311 446 10.4 %RANDOM
Rwork0.224 ---
obs0.224 4281 79 %-
all-10915 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.32 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1--13.16 Å20 Å22.95 Å2
2--15.31 Å20 Å2
3----2.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1432 13 86 1531
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_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.711.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 126 12.7 %
Rwork0.239 434 -
obs--55.2 %
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
Num. reflection obs: 8562 / Num. reflection Rfree: 892 / % reflection Rfree: 8.2 % / Rfactor Rfree: 0.313 / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0045
X-RAY DIFFRACTIONc_angle_deg0.74
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.09

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