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- PDB-7atg: Crystal structure of Z-DNA in complex with putrescinium and potas... -

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Basic information

Entry
Database: PDB / ID: 7atg
TitleCrystal structure of Z-DNA in complex with putrescinium and potassium cations at ultrahigh-resolution
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / Z-DNA / dual-conformation backbone / putrescinium cation / biogenic polyamines / potassium complex
Function / homology4-azaniumylbutylazanium / : / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.6 Å
AuthorsDrozdzal, P. / Gilski, M. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2013/10/M/NZ1/00251 Poland
CitationJournal: Acta Crystallogr.,Sect.B / Year: 2021
Title: Crystal structure of Z-DNA in complex with the polyamine putrescine and potassium cations at ultra-high resolution.
Authors: Drozdzal, P. / Gilski, M. / Jaskolski, M.
History
DepositionOct 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / pdbx_contact_author ...citation / pdbx_contact_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 31, 2024Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,7504
Polymers3,6202
Non-polymers1292
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-6 kcal/mol
Surface area2530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.970, 31.020, 43.860
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: DNA chain DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-58I / 4-azaniumylbutylazanium / Butane-1,4-diyldiammonium / Putrescinium


Mass: 90.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H14N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 1.8 Å3/Da / Density % sol: 31.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10%(v/v) (+/-)-2-methyl-2,4-pentanediol (MPD), 40 mM sodium cacodylate pH 6.0, 80 mM KCl, 12 mM NaCl, 14 mM putrescinium dichloride

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPETRA III, EMBL c/o DESY P13 (MX1)10.7293
SYNCHROTRONPETRA III, EMBL c/o DESY P13 (MX1)20.7293
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 S 6M1PIXELJun 22, 2015
DECTRIS PILATUS3 S 6M2PIXELJun 22, 2015
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.72931
20.72931
ReflectionResolution: 0.6→25.33 Å / Num. obs: 107989 / % possible obs: 90.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 5.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.024 / Rrim(I) all: 0.027 / Χ2: 1.143 / Net I/σ(I): 29.84
Reflection shellResolution: 0.6→0.61 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.88 / Num. unique obs: 1973 / CC1/2: 0.999 / Rrim(I) all: 0.368 / % possible all: 22.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SHELXLrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hig

4hig


Resolution: 0.6→25.33 Å / Num. parameters: 3962 / Num. restraintsaints: 4374 / Cross valid method: FREE R-VALUE
Details: THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. THE FINAL REFINEMENT WAS CALCULATED USING WEIGHTED FULL-MATRIX LEAST-SQUARES ...Details: THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. THE FINAL REFINEMENT WAS CALCULATED USING WEIGHTED FULL-MATRIX LEAST-SQUARES PROCEDURE. CONFORMATION-DEPENDENT GEOMETRICAL RESTRAINTS ON BOND LENGTHS AND BOND ANGLES FOR POLYNUCLEOTIDE CHAINS WERE GENERATED USING THE RESTRAINTLIB SERVER: http://achesym.ibch.poznan.pl/restraintlib/
RfactorNum. reflection% reflectionSelection details
Rfree0.095 1876 1.77 %RANDOM
Rwork0.0877 ---
obs0.0888 106103 90.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso max: 36.87 Å2 / Biso mean: 6.26 Å2 / Biso min: 2.73 Å2
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 141.29 / Occupancy sum non hydrogen: 333.73
Refinement stepCycle: final / Resolution: 0.6→25.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 7 159 406
Biso mean--4.95 12.2 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d1.56
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.005
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.089
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.061
X-RAY DIFFRACTIONs_approx_iso_adps0.07

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