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- PDB-8w7w: Crystal structure of d(CGTATACG)2 with acridine complex -

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Basic information

Entry
Database: PDB / ID: 8w7w
TitleCrystal structure of d(CGTATACG)2 with acridine complex
ComponentsDNA (5'-D(P*CP*GP*TP*AP*TP*AP*CP*G)-3')
KeywordsDNA / Drug-DNA complex / bis-intercalator / acridine
Function / homology: / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsHuang, S.C. / Satange, R.B. / Hou, M.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2628-M-005-001-MY4 Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Targeting DNA junction sites by bis-intercalators induces topological changes with potent antitumor effects.
Authors: Huang, S.C. / Chen, C.W. / Satange, R. / Hsieh, C.C. / Chang, C.C. / Wang, S.C. / Peng, C.L. / Chen, T.L. / Chiang, M.H. / Horng, Y.C. / Hou, M.H.
History
DepositionAug 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(P*CP*GP*TP*AP*TP*AP*CP*G)-3')
B: DNA (5'-D(P*CP*GP*TP*AP*TP*AP*CP*G)-3')
D: DNA (5'-D(P*CP*GP*TP*AP*TP*AP*CP*G)-3')
E: DNA (5'-D(P*CP*GP*TP*AP*TP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,58110
Polymers9,7064
Non-polymers1,8756
Water70339
1
A: DNA (5'-D(P*CP*GP*TP*AP*TP*AP*CP*G)-3')
B: DNA (5'-D(P*CP*GP*TP*AP*TP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7915
Polymers4,8532
Non-polymers9373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-6 kcal/mol
Surface area3940 Å2
MethodPISA
2
D: DNA (5'-D(P*CP*GP*TP*AP*TP*AP*CP*G)-3')
E: DNA (5'-D(P*CP*GP*TP*AP*TP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7915
Polymers4,8532
Non-polymers9373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-6 kcal/mol
Surface area3920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.146, 72.095, 24.127
Angle α, β, γ (deg.)90.00, 92.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 2426.617 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-VZX / ~{N},~{N}'-di(acridin-9-yl)pentane-1,5-diamine


Mass: 456.581 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H28N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.3mM oligonucleotides, 0.3mM ligand, 25mM bis-tris (pH 7.0), 50mM sodium chloride, 10mM magnesium chloride hexahydrate, 15% (v/v) 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→30 Å / Num. obs: 11068 / % possible obs: 96.4 % / Redundancy: 3.6 % / Rsym value: 0.022 / Net I/σ(I): 29.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.58-1.643.60.16910320.9690.9920.1040.1991.07891
1.64-1.73.70.10211560.9920.9980.0620.1191.09699.9
1.7-1.783.70.07511380.9950.9990.0450.0881.05899.7
1.78-1.873.70.05811450.9970.9990.0350.0681.07199.5
1.87-1.993.70.05211240.9960.9990.0320.0611.05199.5
1.99-2.143.70.04511160.9970.9990.0270.0531.07298.8
2.14-2.363.70.03411420.9980.9990.0210.041.07598.4
2.36-2.73.60.02611330.99910.0160.0311.07397.6
2.7-3.43.50.02110610.99910.0130.0251.01293.2
3.4-303.40.01510210.99910.010.0181.0786.8

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→24.12 Å / SU ML: 0.21 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 1113 10.08 %
Rwork0.2183 --
obs0.2193 11047 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→24.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 656 72 39 767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009810
X-RAY DIFFRACTIONf_angle_d1.2631226
X-RAY DIFFRACTIONf_dihedral_angle_d32.979314
X-RAY DIFFRACTIONf_chiral_restr0.051128
X-RAY DIFFRACTIONf_plane_restr0.00936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.650.32981410.26171242X-RAY DIFFRACTION97
1.65-1.740.26031460.23241285X-RAY DIFFRACTION100
1.74-1.840.27311320.23641281X-RAY DIFFRACTION99
1.84-1.990.27821450.24661232X-RAY DIFFRACTION99
1.99-2.190.30851500.26761274X-RAY DIFFRACTION99
2.19-2.50.24941400.24971243X-RAY DIFFRACTION98
2.5-3.150.2811280.26531234X-RAY DIFFRACTION95
3.15-24.120.15211310.16161143X-RAY DIFFRACTION88
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)
10.77720.2534-1.05941.4676-0.21137.3440.3031-0.28830.0642-0.01690.20430.0234-0.16690.4094-0.48270.2406-0.0146-0.01370.2795-0.01240.21458.43411.34880.2452
20.2842-0.2048-0.37020.8555-0.61446.78170.25580.02630.1518-0.10030.1793-0.22160.2869-0.263-0.33770.22470.0139-0.00820.22830.00620.23378.93586.5795-0.4189
36.4226-0.8513-0.52351.08480.17740.8488-0.46410.3963-0.3062-0.02930.14640.03860.0114-0.20430.2710.1823-0.00810.00430.2227-0.01390.168411.718224.9853.6212
45.7647-0.5508-0.31840.7088-0.02140.1319-0.4484-0.06750.3402-0.20030.2131-0.13410.03280.03120.13040.24890.0015-0.02040.20840.00720.218112.343529.7383.1448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 8 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 8 )
3X-RAY DIFFRACTION3chain 'D' and (resid 1 through 8 )
4X-RAY DIFFRACTION4chain 'E' and (resid 1 through 8 )

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