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- PDB-2gw0: A D(TGGGGT)- sodium and calcium complex. -

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Basic information

Entry
Database: PDB / ID: 2gw0
TitleA D(TGGGGT)- sodium and calcium complex.
Components5'-D(*TP*GP*GP*GP*GP*T)-3'
KeywordsDNA / QUADRUPLEX / G-QUADRUPLEX / TETRAPLEX / G-TETRAPLEX / QUADRUPLE HELIX / PARALLEL-STRANDED / D(TGGGGT) / HYDRATED CALCIUM ION / CALCIUM / CALCIUM ION / SODIUM / SODIUM ION.
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLee, M.P.H. / Parkinson, G.N. / Neidle, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: Observation of the coexistence of sodium and calcium ions in a DNA G-quadruplex ion channel.
Authors: Lee, M.P. / Parkinson, G.N. / Hazel, P. / Neidle, S.
History
DepositionMay 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 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 / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,45520
Polymers15,0428
Non-polymers41312
Water3,441191
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)7,86513
Polymers7,5214
Non-polymers3449
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)7,5907
Polymers7,5214
Non-polymers693
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.357, 27.911, 34.969
Angle α, β, γ (deg.)89.11, 75.63, 79.70
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: TETRAHYMENA TELOMERIC SEQUENCE.
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 1.63 Å3/Da / Density % sol: 24.79 %
Crystal growTemperature: 277 K / pH: 6.5
Details: CALCIUM CHLORIDE, DNA, DISTAMYCIN A, SODIUM CHLORIDE, MPD, SPERMINE TETRAHYDROCHLORIDE, SODIUM CACODYLATE BUFFER, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.50
Components of the solutions
IDNameCrystal-IDSol-ID
1CALCIUM CHLORIDE11
2SODIUM CHLORIDE11
3MPD11
4SPERMINE TETRAHYDROCHLORIDE11
5SODIUM CACODYLATE11
6H2O11
7CALCIUM CHLORIDE12
8SODIUM CHLORIDE12
9SODIUM CACODYLATE12
10MPD12

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Data collection

DiffractionMean temperature: 117 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 11, 2003 / Details: OSMIC FOCUSING MIRROR SYSTEM
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.55→25 Å / Num. obs: 12464 / % possible obs: 87.1 % / Observed criterion σ(I): -2 / Redundancy: 2.85 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 27.28
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 8.62 / % possible all: 80

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE FIRST QUADRUPLEX MOLECULE OF NDB ENTRY CODE UDF062 OR PDB ENTRY CODE 352D WITH THYMINES REMOVED.

352d


Resolution: 1.55→8 Å / Num. parameters: 4727 / Num. restraintsaints: 4774 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1234 10.008 %RANDOM
all0.176 12330 --
obs0.174 -92.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 15.62 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1171
Refinement stepCycle: LAST / Resolution: 1.55→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 968 12 191 1171
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.013
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.008
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.019
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.002
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.051
X-RAY DIFFRACTIONs_approx_iso_adps0

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