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- PDB-7bpv: r(GUGGGCCGAC)/d(GTCGGCCCAC) hybrid duplex structure -

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Basic information

Entry
Database: PDB / ID: 7bpv
Titler(GUGGGCCGAC)/d(GTCGGCCCAC) hybrid duplex structure
Components
  • DNA (5'-D(P*GP*TP*CP*GP*GP*CP*CP*CP*AP*C)-3')
  • RNA (5'-R(P*GP*UP*GP*GP*GP*CP*CP*GP*AP*C)-3')
KeywordsDNA-RNA HYBRID / G4C2 repeat / GGCC motif / A-like DNA structure
Function / homologyDNA / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.781 Å
AuthorsWang, S.C. / Satange, R.B. / Hou, M.H.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Targeting the ALS/FTD-associated A-DNA kink with anthracene-based metal complex causes DNA backbone straightening and groove contraction.
Authors: Jhan, C.R. / Satange, R. / Wang, S.C. / Zeng, J.Y. / Horng, Y.C. / Jin, P. / Neidle, S. / Hou, M.H.
History
DepositionMar 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: RNA (5'-R(P*GP*UP*GP*GP*GP*CP*CP*GP*AP*C)-3')
A: DNA (5'-D(P*GP*TP*CP*GP*GP*CP*CP*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3343
Polymers6,2382
Non-polymers961
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-22 kcal/mol
Surface area3900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.348, 46.647, 47.859
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain RNA (5'-R(P*GP*UP*GP*GP*GP*CP*CP*GP*AP*C)-3')


Mass: 3231.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*GP*TP*CP*GP*GP*CP*CP*CP*AP*C)-3')


Mass: 3005.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 5 mM MgSO4, 50 mM Tris HCL, 50 Mm MES (pH-6.5), 2.9 M 1,6-Hexandiol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.78→30 Å / Num. obs: 6395 / % possible obs: 98.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.021 / Rrim(I) all: 0.053 / Χ2: 1.004 / Net I/σ(I): 16.4 / Num. measured all: 40863
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.845.70.4526010.9130.1990.4961.00998
1.84-1.926.40.3476380.9580.1460.3771.00499.8
1.92-26.90.2376350.9820.0960.2561.002100
2-2.116.90.1716190.9850.070.1851.002100
2.11-2.246.90.1386370.9910.0570.1491.009100
2.24-2.426.80.0936470.9910.0390.1011.001100
2.42-2.666.70.0746450.9950.0310.0811.002100
2.66-3.046.20.0626520.9960.0270.0681.008100
3.04-3.835.60.0466460.9970.0210.051197.7
3.83-305.70.0376750.9980.0170.041193.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L75

6l75


Resolution: 1.781→21.614 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.87
RfactorNum. reflection% reflection
Rfree0.2378 642 10.09 %
Rwork0.218 --
obs0.22 6361 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157.5 Å2 / Biso mean: 44.3265 Å2 / Biso min: 30.8 Å2
Refinement stepCycle: final / Resolution: 1.781→21.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 421 5 17 443
Biso mean--83.16 47.77 -
Num. residues----20
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.781-1.91830.27881250.255110598
1.9183-2.11120.34081200.27321128100
2.1112-2.41640.28651340.27311149100
2.4164-3.0430.31851290.28931169100
3.043-21.610.19031340.1778116896
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)
10.2044-0.67480.89344.6189-2.52833.88-0.01920.14530.0833-0.0797-0.03810.02530.10610.00470.10390.29190.014-0.02040.42170.00890.3542-5.9934-2.109111.4575
20.6419-1.16921.04152.3621-2.98916.66310.0301-0.03450.025-0.0191-0.1042-0.10110.43770.1890.04190.35930.0244-0.00340.3320.01280.3956-2.6663-3.022711.6796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'S' and (resid 1 through 10 )S1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 1 through 10 )A1 - 10

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