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- PDB-6s7d: Self-complementary duplex DNA containing an internucleoside phosp... -

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Basic information

Entry
Database: PDB / ID: 6s7d
TitleSelf-complementary duplex DNA containing an internucleoside phosphoroselenolate
ComponentsDNA (5'-D(*GP*(XCI)P*CP*CP*CP*GP*GP*GP*AP*C)-3')
KeywordsDNA / Modified Phasing Duplex Phosphoroselenolate
Function / homology: / SPERMINE / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsConlon, P.F. / Steinhogl, J. / Vyle, J.S. / Hall, J.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/C00776X/1 United Kingdom
CitationJournal: Chem Sci / Year: 2019
Title: Solid-phase synthesis and structural characterisation of phosphoroselenolate-modified DNA: a backbone analogue which does not impose conformational bias and facilitates SAD X-ray crystallography.
Authors: Conlon, P.F. / Eguaogie, O. / Wilson, J.J. / Sweet, J.S.T. / Steinhoegl, J. / Englert, K. / Hancox, O.G.A. / Law, C.J. / Allman, S.A. / Tucker, J.H.R. / Hall, J.P. / Vyle, J.S.
History
DepositionJul 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,7448
Polymers6,1862
Non-polymers5586
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-64 kcal/mol
Surface area3450 Å2
Unit cell
Length a, b, c (Å)38.642, 38.642, 79.307
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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DNA chain , 1 types, 2 molecules AB

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


Mass: 3092.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 66 molecules

#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: The crystallization solution contained 1 uL of 2 mM oligonucleotide and 6 uL of a solution containing 10% (v/v) 2-methyl-2,4-pentanediol, 40 mM Na-cacodylate pH 6, 12 mM Spermine tetra-HCl, ...Details: The crystallization solution contained 1 uL of 2 mM oligonucleotide and 6 uL of a solution containing 10% (v/v) 2-methyl-2,4-pentanediol, 40 mM Na-cacodylate pH 6, 12 mM Spermine tetra-HCl, 80 mM NaCl and 20 mM BaCl2. This was equilibrated against 100 uL of 35% (v/v) 2-methyl-2,4-pentanediol. Crystals grew in approximately 1-2 weeks and were grown using the sitting-drop method at 291 K.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9596 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 18, 2019
RadiationMonochromator: Dual Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9596 Å / Relative weight: 1
ReflectionResolution: 1.45→25.57 Å / Num. obs: 12548 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Redundancy: 3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.032 / Rrim(I) all: 0.06 / Net I/σ(I): 12.5
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.556 / Num. unique obs: 625 / CC1/2: 0.741 / Rpim(I) all: 0.375 / Rrim(I) all: 0.674 / % possible all: 98.7

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.16_3549refinement
xia2data scaling
DIALSdata reduction
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→25.57 Å / Cross valid method: FREE R-VALUE / σ(F): 3.79 / Phase error: 25.2935
RfactorNum. reflection% reflection
Rfree0.2366 579 4.62 %
Rwork0.1849 --
obs0.1919 12530 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.54 Å2
Refinement stepCycle: LAST / Resolution: 1.45→25.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 19 60 483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089463
X-RAY DIFFRACTIONf_angle_d0.9357698
X-RAY DIFFRACTIONf_chiral_restr0.078576
X-RAY DIFFRACTIONf_plane_restr0.009220
X-RAY DIFFRACTIONf_dihedral_angle_d20.1052197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.590.33321230.27292953X-RAY DIFFRACTION95.01
1.59-1.820.25181330.2342930X-RAY DIFFRACTION94.52
1.82-2.280.26691660.2152932X-RAY DIFFRACTION93.47
2.28-7.410.21451490.16133033X-RAY DIFFRACTION92.72

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