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- PDB-7u38: Pixantrone tethered DNA duplex -

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Basic information

Entry
Database: PDB / ID: 7u38
TitlePixantrone tethered DNA duplex
ComponentsPixantrone AP conjugate-modified DNA
KeywordsDNA / Pixantrone / DNA structure / Pixantrone-AP / pixantrone conjugate / abasic site
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.49 Å
AuthorsPallan, P.S. / Egli, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA-160032 United States
CitationJournal: To Be Published
Title: Structural Characterization of a Covalent Conjugate between Pixantrone and an Abasic Site in DNA
Authors: Kellum Jr., A.H. / Pallan, P.S. / Terrell, J.T. / Fu, Y. / Noh, B. / Rizzo, C.J. / Egli, M. / Stone, M.P.
History
DepositionFeb 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 2.0May 22, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pixantrone AP conjugate-modified DNA
B: Pixantrone AP conjugate-modified DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0856
Polymers7,8372
Non-polymers2484
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.921, 95.921, 73.118
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11B-214-

HOH

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Components

#1: DNA chain Pixantrone AP conjugate-modified DNA


Mass: 3918.543 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: LVR is Pixantrone AP conjugate, CBR is 5-Bromo cytidine
Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystallized from drops containing 2.2 M ammonium sulfate, and 2.8% to 3.8% PEG-400, in 0.1 M HEPES sodium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 22, 2020
RadiationMonochromator: Kohzu monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 7367 / % possible obs: 99.9 % / Redundancy: 37.5 % / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.022 / Rrim(I) all: 0.133 / Χ2: 0.816 / Net I/σ(I): 3.9 / Num. measured all: 276573
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.49-2.5837.91.2127100.9170.1981.2290.364100
2.58-2.6840.70.9217200.9520.1440.9320.378100
2.68-2.840.40.5987220.9740.0940.6060.415100
2.8-2.9539.80.4897070.9860.0770.4950.433100
2.95-3.1439.40.2357160.9970.0370.2380.509100
3.14-3.3838.40.117320.9990.0180.1120.753100
3.38-3.7238.10.17360.9990.0160.1020.804100
3.72-4.2634.40.1067390.9990.0180.1070.838100
4.26-5.3630.40.1087500.9980.020.111.87199.2
5.36-5036.40.0878350.9990.0140.0881.933100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.49→27.71 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.2 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 537 7.4 %RANDOM
Rwork0.245 ---
obs0.2462 6740 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 156.38 Å2 / Biso mean: 49.563 Å2 / Biso min: 5.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.09 Å2-0 Å2
2--0.19 Å20 Å2
3----0.61 Å2
Refinement stepCycle: final / Resolution: 2.49→27.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 506 16 27 549
Biso mean--77.38 39.53 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.013575
X-RAY DIFFRACTIONr_bond_other_d0.0040.021314
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.513864
X-RAY DIFFRACTIONr_angle_other_deg1.3372.956734
X-RAY DIFFRACTIONr_chiral_restr0.0630.269
X-RAY DIFFRACTIONr_gen_planes_refined0.0410.021311
X-RAY DIFFRACTIONr_gen_planes_other0.010.021126
LS refinement shellResolution: 2.492→2.557 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.483 38 -
Rwork0.62 487 -
all-525 -
obs--99.62 %

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