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- PDB-6qjs: Crystal structure of a DNA dodecamer containing a tetramethylpipe... -

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Basic information

Entry
Database: PDB / ID: 6qjs
TitleCrystal structure of a DNA dodecamer containing a tetramethylpiperidinoxyl (nitroxide) spin label
ComponentsDNA (5'-D(P*GP*CP*AP*AP*AP*TP*TP*(S6M)P*GP*CP*G)-3')
KeywordsDNA / Nitroxide / Spin label / Tetramethylpiperidinoxyl
Function / homologyCOBALT HEXAMMINE(III) / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHardwick, J.S. / Haugland, M.M. / Ptchelkine, D. / Brown, T. / Anderson, E.E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/M019195/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J001694/1 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: 2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis.
Authors: Hardwick, J.S. / Haugland, M.M. / El-Sagheer, A.H. / Ptchelkine, D. / Beierlein, F.R. / Lane, A.N. / Brown, T. / Lovett, J.E. / Anderson, E.A.
History
DepositionJan 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 / _struct_conn.ptnr2_symmetry
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(P*GP*CP*AP*AP*AP*TP*TP*(S6M)P*GP*CP*G)-3')
B: DNA (5'-D(P*GP*CP*AP*AP*AP*TP*TP*(S6M)P*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3866
Polymers7,7412
Non-polymers6444
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-7 kcal/mol
Surface area4820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.999, 42.999, 97.493
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: DNA chain DNA (5'-D(P*GP*CP*AP*AP*AP*TP*TP*(S6M)P*GP*CP*G)-3')


Mass: 3870.665 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: 3.36 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Potassium chloride (10 mM), sodium chloride (80 mM), magnesium chloride (20 mM), sodium cacodylate (40 mM, pH 5.5), MPD (35% v/v), Hexammine cobalt(III) chloride (2 mM)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97935 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.481
11-h,-k,l20.519
ReflectionResolution: 1.8→37.24 Å / Num. obs: 9926 / % possible obs: 97.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.3
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.589

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1s2r

1s2r


Resolution: 1.8→37.24 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.883 / SU B: 1.849 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25138 555 5.6 %RANDOM
Rwork0.21307 ---
obs0.21532 9365 96.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.733 Å2
Baniso -1Baniso -2Baniso -3
1-10.14 Å20 Å20 Å2
2--10.14 Å20 Å2
3----20.29 Å2
Refinement stepCycle: 1 / Resolution: 1.8→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 484 28 7 519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.012566
X-RAY DIFFRACTIONr_bond_other_d0.0020.02354
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.54882
X-RAY DIFFRACTIONr_angle_other_deg1.2873804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1190.276
X-RAY DIFFRACTIONr_gen_planes_refined0.030.02278
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02112
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8473.498566
X-RAY DIFFRACTIONr_scbond_other3.8443.499567
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2055.221883
X-RAY DIFFRACTIONr_long_range_B_refined6.36632.765744
X-RAY DIFFRACTIONr_long_range_B_other6.36632.77744
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.797→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 32 -
Rwork0.252 657 -
obs--94.13 %

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