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- PDB-352d: THE CRYSTAL STRUCTURE OF A PARALLEL-STRANDED PARALLEL-STRANDED GU... -

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Basic information

Entry
Database: PDB / ID: 352d
TitleTHE CRYSTAL STRUCTURE OF A PARALLEL-STRANDED PARALLEL-STRANDED GUANINE TETRAPLEX AT 0.95 ANGSTROM RESOLUTION
ComponentsDNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
KeywordsDNA / U-DNA / QUADRUPLE HELIX / PARALLEL-STRANDED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.95 Å
AuthorsPhillips, K. / Dauter, Z. / Murchie, A.I.H. / Lilley, D.M.J. / Luisi, B.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: The crystal structure of a parallel-stranded guanine tetraplex at 0.95 A resolution.
Authors: Phillips, K. / Dauter, Z. / Murchie, A.I. / Lilley, D.M. / Luisi, B.
History
DepositionSep 4, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Nov 10, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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.ptnr1_symmetry / _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: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
B: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
C: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
D: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
E: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
F: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
G: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
H: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
I: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
J: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
K: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
L: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
M: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
N: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
O: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
P: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,76739
Polymers30,08416
Non-polymers68323
Water10,088560
1
A: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
B: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
C: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
D: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,77312
Polymers7,5214
Non-polymers2528
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
F: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
G: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
H: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6308
Polymers7,5214
Non-polymers1094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
J: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
K: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
L: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6539
Polymers7,5214
Non-polymers1325
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
N: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
O: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
P: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,71010
Polymers7,5214
Non-polymers1896
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.280, 34.780, 56.230
Angle α, β, γ (deg.)74.31, 77.68, 89.81
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 1880.251 Da / Num. of mol.: 16 / Source method: obtained synthetically
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.73 Å3/Da / Density % sol: 28.75 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: pH 6.60, VAPOR DIFFUSION, HANGING DROP, temperature 278.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4CACL211
5SPERMINE_HCL11
6NACL11
7WATER12
8MPD12
9NA CACODYLATE12
10CACL212
11SPERMINE_HCL12
12NACL12
Crystal grow
*PLUS
Temperature: 4-6 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMsodium cacodylate-HCl1drop
212 mM1dropCaCl2
36 mMspermine tetrahydrochloride1drop
4130-180 mM1dropNaCl
55 %(v/v)MPD1drop
61 mMd(TG4T)1drop
7120 mMsodium cacodylate-HCl1reservoir
870 mM1reservoirCaCl2
90.7-1 M1reservoirNaCl
1026-32 %MPD1reservoir
111
121

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONEMBL/DESY, HAMBURG BW7B1
SYNCHROTRONSRS PX9.52
Radiation
IDMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Mx-ray1
2Mx-ray2
Radiation wavelength
IDRelative weight
11
21
ReflectionHighest resolution: 0.95 Å / Num. obs: 112719 / % possible obs: 88.8 %
Reflection
*PLUS
% possible obs: 88.8 % / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
Highest resolution: 0.95 Å / Lowest resolution: 0.97 Å / % possible obs: 85.9 % / Num. unique obs: 5470 / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 5.5

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Processing

Software
NameClassification
SHELXL93refinement
DENZOdata reduction
SHELXL-93refinement
RefinementStarting model: NDB ENTRY UDF063 (PDB ENTRY 244D)

244d


Highest resolution: 0.95 Å / σ(F): 0 /
RfactorNum. reflection
obs0.152 112719
all-112719
Refinement stepCycle: LAST / Highest resolution: 0.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1907 23 560 2490

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