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- PDB-6qjo: DNA containing both right- and left-handed parallel-stranded G-qu... -

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Basic information

Entry
Database: PDB / ID: 6qjo
TitleDNA containing both right- and left-handed parallel-stranded G-quadruplexes
ComponentsDNA (28-MER)
KeywordsDNA / G-quadruplex left-handed right-handed
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWinnerdy, F.R. / Bakalar, B. / Maity, A. / Vandana, J.J. / Schmitt, E. / Mechulam, Y. / Phan, A.T.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: NMR solution and X-ray crystal structures of a DNA molecule containing both right- and left-handed parallel-stranded G-quadruplexes.
Authors: Winnerdy, F.R. / Bakalar, B. / Maity, A. / Vandana, J.J. / Mechulam, Y. / Schmitt, E. / Phan, A.T.
History
DepositionJan 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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
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_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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (28-MER)
B: DNA (28-MER)
C: DNA (28-MER)
D: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,17719
Polymers35,5914
Non-polymers58615
Water2,990166
1
A: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0545
Polymers8,8981
Non-polymers1564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0154
Polymers8,8981
Non-polymers1173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0545
Polymers8,8981
Non-polymers1564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0545
Polymers8,8981
Non-polymers1564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.120, 39.270, 53.550
Angle α, β, γ (deg.)90.04, 93.03, 89.95
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain
DNA (28-MER)


Mass: 8897.662 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 1.82 Å3/Da / Density % sol: 32.54 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 60% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 22501 / % possible obs: 95.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 25.3 Å2 / CC1/2: 0.99 / Rsym value: 0.115 / Net I/σ(I): 10.45
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.72 % / Mean I/σ(I) obs: 5.8 / Num. unique obs: 3079 / CC1/2: 0.818 / Rsym value: 0.359 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U5M

4u5m


Resolution: 1.8→39.27 Å / Cross valid method: FREE R-VALUE / σ(F): 2.77 / Phase error: 24.09
RfactorNum. reflection% reflection
Rfree0.2019 1131 5.03 %
Rwork0.1642 --
obs0.1717 22497 95.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2364 15 166 2545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172652
X-RAY DIFFRACTIONf_angle_d1.3554116
X-RAY DIFFRACTIONf_dihedral_angle_d38.3351104
X-RAY DIFFRACTIONf_chiral_restr0.073444
X-RAY DIFFRACTIONf_plane_restr0.011112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8014-1.88330.2651210.26332366X-RAY DIFFRACTION82
1.8833-1.98230.22771330.25832740X-RAY DIFFRACTION92
1.9823-2.10610.28671400.2482700X-RAY DIFFRACTION92
2.1061-2.26820.27191470.22752700X-RAY DIFFRACTION93
2.2682-2.49530.23591590.20042690X-RAY DIFFRACTION92
2.4953-2.85390.2221140.16992761X-RAY DIFFRACTION94
2.8539-3.58620.16721240.14222698X-RAY DIFFRACTION92
3.5862-14.29240.16951520.11382670X-RAY DIFFRACTION92

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