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- PDB-6m5j: U shaped head to head four-way junction in d(TTCTGCTGCTGAA/TTCTGC... -

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Basic information

Entry
Database: PDB / ID: 6m5j
TitleU shaped head to head four-way junction in d(TTCTGCTGCTGAA/TTCTGCAGCTGAA) sequence
Components
  • DNA (5'-D(P*TP*TP*CP*TP*GP*CP*AP*GP*CP*TP*GP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*CP*TP*GP*CP*TP*GP*CP*TP*GP*AP*A)-3')
KeywordsDNA / T:T mismatch / CTG repeat / four-way junction / triaminotriazine-acridine conjugate
Function / homology: / Chem-F1R / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHou, M.H. / Chien, C.M. / Satange, R.B.
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Structural Basis for Targeting T:T Mismatch with Triaminotriazine-Acridine Conjugate Induces a U-Shaped Head-to-Head Four-Way Junction in CTG Repeat DNA.
Authors: Chien, C.M. / Wu, P.C. / Satange, R. / Chang, C.C. / Lai, Z.L. / Hagler, L.D. / Zimmerman, S.C. / Hou, M.H.
History
DepositionMar 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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 (5'-D(P*TP*TP*CP*TP*GP*CP*TP*GP*CP*TP*GP*AP*A)-3')
B: DNA (5'-D(P*TP*TP*CP*TP*GP*CP*AP*GP*CP*TP*GP*AP*A)-3')
C: DNA (5'-D(P*TP*TP*CP*TP*GP*CP*TP*GP*CP*TP*GP*AP*A)-3')
D: DNA (5'-D(P*TP*TP*CP*TP*GP*CP*TP*GP*CP*TP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,83112
Polymers15,8394
Non-polymers1,9918
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-66 kcal/mol
Surface area8900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.630, 62.086, 30.747
Angle α, β, γ (deg.)90.000, 121.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain DNA (5'-D(P*TP*TP*CP*TP*GP*CP*TP*GP*CP*TP*GP*AP*A)-3')


Mass: 3957.583 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*TP*TP*CP*TP*GP*CP*AP*GP*CP*TP*GP*AP*A)-3')


Mass: 3966.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-F1R / N4-[4-[(6-chloranyl-2-methoxy-acridin-9-yl)amino]butyl]-1,3,5-triazine-2,4,6-triamine


Mass: 438.913 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H23ClN8O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: MES (pH=6.5) 50 mM, KCl 200 mM, MPD 35%, CoCl2 10 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.64→30 Å / Num. obs: 11117 / % possible obs: 97.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.028 / Rrim(I) all: 0.053 / Χ2: 1.027 / Net I/σ(I): 21.8 / Num. measured all: 37937
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.64-1.72.80.2310380.9430.1560.2791.04691.9
1.7-1.772.90.20810600.9440.1420.2531.02394.2
1.77-1.853.10.16711090.9740.1120.2031.01798.3
1.85-1.943.40.16511100.9740.1080.1981.02999.6
1.94-2.073.60.1311140.9870.080.1531.014100
2.07-2.233.70.10311620.9930.0630.1211.007100
2.23-2.453.70.07811000.9970.0480.0921.05599.8
2.45-2.83.70.05111430.9970.0310.061.04299.4
2.8-3.533.60.03111550.9990.0190.0371.03599
3.53-303.50.02911260.9980.0180.0341.00995.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M4T

6m4t


Resolution: 1.65→19.221 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.92
RfactorNum. reflection% reflection
Rfree0.2077 522 4.83 %
Rwork0.1867 --
obs0.1876 10816 50 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 56.14 Å2 / Biso mean: 29.3128 Å2 / Biso min: 17.61 Å2
Refinement stepCycle: final / Resolution: 1.65→19.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1061 128 167 1356
Biso mean--26.21 29.48 -
Num. residues----51
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6503-1.81630.22761490.1939245447
1.8163-2.07880.20831270.1933260150
2.0788-2.6180.27371190.221264850
2.618-19.2210.18241270.172259148

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