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- PDB-6a85: Crystal structure of a novel DNA quadruplex -

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Basic information

Entry
Database: PDB / ID: 6a85
TitleCrystal structure of a novel DNA quadruplex
ComponentsDNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*GP*GP*GP*TP*GP*CP*GP*TP*T)-3')
KeywordsDNA / quadruplex
Function / homology: / AMMONIUM ION / LEAD (II) ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsLiu, H.H. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370728 China
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: High-resolution DNA quadruplex structure containing all the A-, G-, C-, T-tetrads.
Authors: Liu, H.H. / Wang, R. / Yu, X. / Shen, F.S. / Lan, W.X. / Haruehanroengra, P. / Yao, Q.Q. / Zhang, J. / Chen, Y.Q. / Li, S.H. / Wu, B.X. / Zheng, L.N. / Ma, J.B. / Lin, J.Z. / Cao, C.Y. / Li, ...Authors: Liu, H.H. / Wang, R. / Yu, X. / Shen, F.S. / Lan, W.X. / Haruehanroengra, P. / Yao, Q.Q. / Zhang, J. / Chen, Y.Q. / Li, S.H. / Wu, B.X. / Zheng, L.N. / Ma, J.B. / Lin, J.Z. / Cao, C.Y. / Li, J.X. / Sheng, J. / Gan, J.H.
History
DepositionJul 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*GP*GP*GP*TP*GP*CP*GP*TP*T)-3')
B: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*GP*GP*GP*TP*GP*CP*GP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,18717
Polymers10,6952
Non-polymers49215
Water2,720151
1
A: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*GP*GP*GP*TP*GP*CP*GP*TP*T)-3')
B: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*GP*GP*GP*TP*GP*CP*GP*TP*T)-3')
hetero molecules

A: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*GP*GP*GP*TP*GP*CP*GP*TP*T)-3')
B: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*GP*GP*GP*TP*GP*CP*GP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,37434
Polymers21,3904
Non-polymers98430
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area13190 Å2
ΔGint-301 kcal/mol
Surface area6200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.822, 46.651, 51.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-101-

LI

21A-102-

LI

31A-103-

NA

41A-104-

NA

51A-105-

NA

61A-106-

NA

71A-107-

NA

81A-108-

NA

91A-109-

NA

101A-110-

NA

111A-111-

NA

121A-112-

PB

131A-113-

NA

141B-101-

NA

151B-102-

NH4

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Components

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DNA chain , 1 types, 2 molecules AB

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


Mass: 5347.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 166 molecules

#2: Chemical ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PB / LEAD (II) ION / Lead


Mass: 207.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pb
#5: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.12 Å3/Da / Density % sol: 41.88 % / Description: Rod
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 100mM CAPS-NaOH pH 10.5, 200mM Li2SO4, 2.0M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 16016 / % possible obs: 96.1 % / Redundancy: 12.8 % / Rsym value: 0.076 / Net I/σ(I): 64.8
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 11.5 % / Num. unique obs: 1424 / Rsym value: 0.262 / % possible all: 87.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→25.496 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.08
RfactorNum. reflection% reflection
Rfree0.1689 785 4.92 %
Rwork0.1364 --
obs0.138 15970 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→25.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 712 15 151 878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009802
X-RAY DIFFRACTIONf_angle_d1.1691240
X-RAY DIFFRACTIONf_dihedral_angle_d31.769332
X-RAY DIFFRACTIONf_chiral_restr0.053134
X-RAY DIFFRACTIONf_plane_restr0.01534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4504-1.54130.18531300.14062322X-RAY DIFFRACTION90
1.5413-1.66030.17411100.12432552X-RAY DIFFRACTION97
1.6603-1.82730.15241210.12352561X-RAY DIFFRACTION98
1.8273-2.09160.16911380.13452572X-RAY DIFFRACTION99
2.0916-2.63480.15621430.14462616X-RAY DIFFRACTION99
2.6348-25.49980.17731430.13842562X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.56390.21340.19430.7383-0.10273.0666-0.0119-0.0843-0.02080.09460.06370.0197-0.0712-0.1678-0.05160.09410.03760.00250.09640.00650.112817.25080.2827-16.5036
20.5134-0.0544-0.69450.3463-0.19872.1012-0.0325-0.06520.0380.0930.07230.0051-0.12690.1472-0.0420.1070.0101-0.00590.07920.00020.112619.95262.117-15.6118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:17)
2X-RAY DIFFRACTION2(chain B and resseq 1:17)

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