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- PDB-5dww: Structural Insights into the Quadruplex-Duplex 3' Interface forme... -

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Basic information

Entry
Database: PDB / ID: 5dww
TitleStructural Insights into the Quadruplex-Duplex 3' Interface formed from a Telomeric Repeat - TTLOOP
Components
  • DNA (25-MER)
  • DNA (5'-D(*TP*AP*AP*CP*GP*CP*TP*A)-3')
KeywordsDNA / Telomere / Quadruplex / Junction / Duplex
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsRusso Krauss, I. / Parkinson, G.N.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Structural Insights into the Quadruplex-Duplex 3' Interface Formed from a Telomeric Repeat: A Potential Molecular Target.
Authors: Russo Krauss, I. / Ramaswamy, S. / Neidle, S. / Haider, S. / Parkinson, G.N.
History
DepositionSep 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Jan 10, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (25-MER)
B: DNA (5'-D(*TP*AP*AP*CP*GP*CP*TP*A)-3')
C: DNA (25-MER)
D: DNA (5'-D(*TP*AP*AP*CP*GP*CP*TP*A)-3')
E: DNA (25-MER)
F: DNA (5'-D(*TP*AP*AP*CP*GP*CP*TP*A)-3')
G: DNA (25-MER)
H: DNA (5'-D(*TP*AP*AP*CP*GP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,68618
Polymers41,2958
Non-polymers39110
Water00
1
A: DNA (25-MER)
B: DNA (5'-D(*TP*AP*AP*CP*GP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4415
Polymers10,3242
Non-polymers1173
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (25-MER)
D: DNA (5'-D(*TP*AP*AP*CP*GP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4024
Polymers10,3242
Non-polymers782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DNA (25-MER)
F: DNA (5'-D(*TP*AP*AP*CP*GP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4415
Polymers10,3242
Non-polymers1173
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: DNA (25-MER)
H: DNA (5'-D(*TP*AP*AP*CP*GP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4024
Polymers10,3242
Non-polymers782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: DNA (25-MER)
F: DNA (5'-D(*TP*AP*AP*CP*GP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4415
Polymers10,3242
Non-polymers1173
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint2 kcal/mol
Surface area5960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.610, 101.230, 145.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: DNA chain
DNA (25-MER)


Mass: 7913.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain
DNA (5'-D(*TP*AP*AP*CP*GP*CP*TP*A)-3')


Mass: 2410.618 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 2 M lithium sulphate, 50 mM Tris/HCl pH 8.8, 2 mM CuCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.79→45.56 Å / Num. obs: 12767 / % possible obs: 95.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.9
Reflection shellResolution: 2.79→2.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.679 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DWX

5dwx


Resolution: 2.79→45 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 24.309 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 1 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25268 623 4.9 %RANDOM
Rwork0.21548 ---
obs0.2173 12004 94.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 103.414 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--0.21 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.79→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2723 10 0 2733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0113055
X-RAY DIFFRACTIONr_bond_other_d0.0030.021486
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.1544719
X-RAY DIFFRACTIONr_angle_other_deg2.89233524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.160.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021611
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02620
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.2158.1093047
X-RAY DIFFRACTIONr_scbond_other6.2148.1093048
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.36412.1344717
X-RAY DIFFRACTIONr_long_range_B_refined13.09776.2354826
X-RAY DIFFRACTIONr_long_range_B_other13.09676.2354827
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.566 47 -
Rwork0.413 898 -
obs--98.13 %
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)
13.58190.3236-1.19822.2504-0.45843.21650.09770.3574-0.2048-0.2718-0.01550.0301-0.0413-0.1098-0.08230.23560.0521-0.01270.19-0.02410.04185.969-0.09725.423
21.823-0.3961-2.06110.13170.25215.94490.0458-0.69420.02980.08330.1434-0.02930.08550.477-0.18920.3472-0.0345-0.06990.4130.01740.093787.694-0.02147.773
31.0735-1.32160.97831.6279-1.13037.34760.03740.14810.0198-0.0434-0.1877-0.0252-0.1201-0.22520.15030.2277-0.0553-0.04390.2466-0.01030.036484.616-0.51513.293
42.7755-0.1868-0.26190.78881.44784.9268-0.12550.38520.2712-0.4631-0.0718-0.0562-0.496-0.11860.19730.35960.0060.02610.06310.06350.1787107.39621.47425.388
50.1669-0.2232-1.06840.6161.2317.4393-0.046-0.0693-0.00490.39850.01250.030.02060.15610.03350.3869-0.0145-0.01430.2915-0.04520.1857106.72419.61947.92
63.01591.7958-2.22622.29322.052811.06630.3129-0.3783-0.1410.1933-0.0645-0.2135-0.23270.5567-0.24850.29340.0437-0.09180.3629-0.02150.042789.170.73659.778
71.3530.6669-3.44420.5156-1.6818.82160.03430.09670.04640.05560.07070.0184-0.1609-0.1731-0.1050.1858-0.0251-0.01840.20830.05860.0598107.41922.58813.828
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 25
2X-RAY DIFFRACTION2A1 - 25
3X-RAY DIFFRACTION3D1 - 8
4X-RAY DIFFRACTION4G1 - 25
5X-RAY DIFFRACTION5E1 - 25
6X-RAY DIFFRACTION6B1 - 8
7X-RAY DIFFRACTION7H1 - 8

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