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- PDB-244d: THE HIGH-RESOLUTION CRYSTAL STRUCTURE OF A PARALLEL-STRANDED GUAN... -

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Basic information

Entry
Database: PDB / ID: 244d
TitleTHE HIGH-RESOLUTION CRYSTAL STRUCTURE OF A PARALLEL-STRANDED GUANINE TETRAPLEX
ComponentsDNA (5'-D(*TP*GP*GP*GP*GP*T)-3')
KeywordsDNA / UNUSUAL DNA / QUADRUPLE HELIX / PARALLEL-STRANDED TETRAPLEX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.2 Å
AuthorsLaughlan, G. / Murchie, A.I.H. / Norman, D.G. / Moore, M.H. / Moody, P.C.E. / Lilley, D.M.J. / Luisi, B.
CitationJournal: Science / Year: 1994
Title: The high-resolution crystal structure of a parallel-stranded guanine tetraplex.
Authors: Laughlan, G. / Murchie, A.I. / Norman, D.G. / Moore, M.H. / Moody, P.C. / Lilley, D.M. / Luisi, B.
History
DepositionOct 19, 1995Deposition site: NDB / Processing site: NDB
Revision 1.0Feb 23, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 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

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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
Water9,260514
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)7,81313
Polymers7,5214
Non-polymers2929
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)7,5907
Polymers7,5214
Non-polymers693
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)28.760, 35.470, 56.770
Angle α, β, γ (deg.)74.39, 77.64, 89.73
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.: 514 / 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: 1.81 Å3/Da / Density % sol: 31.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: pH 6.60, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4CACL211
5NACL11
6SPERMINE11
7WATER12
8MPD12
9NA CACODYLATE12
10CACL212
11SPERMINE12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMNa cacodylate-HCl1drop
212 mM1dropCaCl2
36 mMspermine1drop
4130-180 mM1dropNaCl
55 %(v/v)MPD1drop
61 mMTG4T1drop
7120 mMsodium cacodylate-HCl1reservoir
870 mM1reservoirCaCl2
9700-1000 mM1reservoirNaCl
1032 %MPD1reservoir
111

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Data collection

DiffractionMean temperature: 277 K
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.2 Å / Num. obs: 65264 / % possible obs: 76.9 %
Reflection
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 3.16 Å / % possible obs: 97.7 % / Num. measured all: 211674 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 1.29 Å / % possible obs: 95.5 % / Num. unique obs: 13162 / Num. measured obs: 24851 / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameClassification
SHELX-93refinement
DENZOdata reduction
CCP4data reduction
RefinementResolution: 1.2→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.176 --
obs0.124 65264 97.7 %
all-65264 -
Refinement stepCycle: LAST / Resolution: 1.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1916 23 514 2453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 8 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_deg / Dev ideal: 1.6

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