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- PDB-4l0a: X-ray structure of an all LNA quadruplex -

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Basic information

Entry
Database: PDB / ID: 4l0a
TitleX-ray structure of an all LNA quadruplex
ComponentsDNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
KeywordsDNA / RNA / parallel G-quadruplex / locked nucleic acid (LNA)
Function / homology: / DNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRusso Krauss, I. / Parkinson, G. / Merlino, A. / Mazzarella, L. / Sica, F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: A regular thymine tetrad and a peculiar supramolecular assembly in the first crystal structure of an all-LNA G-quadruplex.
Authors: Russo Krauss, I. / Parkinson, G.N. / Merlino, A. / Mattia, C.A. / Randazzo, A. / Novellino, E. / Mazzarella, L. / Sica, F.
History
DepositionMay 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
B: DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
C: DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
D: DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
E: DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
F: DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
G: DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
H: DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,04017
Polymers13,5298
Non-polymers5119
Water4,252236
1
A: DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
B: DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
C: DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
D: DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9748
Polymers6,7644
Non-polymers2094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
F: DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
G: DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
H: DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0669
Polymers6,7644
Non-polymers3015
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.670, 27.670, 196.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: DNA/RNA hybrid
DNA/RNA (5'-R(*(TLN)P*(LCG)P*(LCG)P*(LCG)P*(TLN))-3')


Mass: 1691.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: locked nucleic acid 5'-TGGGT-3'
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 1.61 Å3/Da / Density % sol: 23.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 2.0 M ammonium sulphate, 10 mM magnesium sulphate, 50 mM sodium cacodilate, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 9327 / Num. obs: 8969 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 7.7 / % possible all: 74.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S9L

1s9l


Resolution: 1.7→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.18 472 random
Rwork0.16 --
all0.16 8969 -
obs0.16 8945 -
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 904 24 236 1164

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