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- PDB-5w20: Crystal Structure of inosine-substituted duplex DNA -

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Basic information

Entry
Database: PDB / ID: 5w20
TitleCrystal Structure of inosine-substituted duplex DNA
ComponentsDNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*TP*GP*G)-3')
KeywordsDNA / Inosine / DNA crystal structure / deoxyinonsine / circular dichroism of modified DNA
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.36 Å
AuthorsPallan, P.S. / Egli, M.
CitationJournal: J. Biomol. Struct. Dyn. / Year: 2018
Title: Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography.
Authors: Peters, J.P. / Kowal, E.A. / Pallan, P.S. / Egli, M. / Maher 3rd., L.J.
History
DepositionJun 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 13, 2017Group: Database references / Category: citation / Item: _citation.page_last
Revision 1.3Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.4Mar 13, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,1788
Polymers6,0322
Non-polymers1466
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-33 kcal/mol
Surface area3930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.190, 35.043, 41.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3015.965 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Droplets (2 uL) containing oligonucleotide (0.23 mM), sodium cacodylate (25 mM, pH 6.5), magnesium acetate (12.5 mM), and 2-methyl-2,4-pentanediol (MPD, 20% v/v) that were equilibrated ...Details: Droplets (2 uL) containing oligonucleotide (0.23 mM), sodium cacodylate (25 mM, pH 6.5), magnesium acetate (12.5 mM), and 2-methyl-2,4-pentanediol (MPD, 20% v/v) that were equilibrated against a 1 mL reservoir of sodium cacodylate (50 mM, pH 6.5), magnesium acetate (25 mM), and MPD (40%) v/v)
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2015
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.36→50 Å / Num. obs: 11019 / % possible obs: 99.1 % / Observed criterion σ(I): 5 / Redundancy: 7.7 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.035 / Net I/σ(I): 30.57
Reflection shellResolution: 1.36→1.41 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.343 / Num. unique obs: 1002 / Rpim(I) all: 0.133 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.36→26.73 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.87 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 569 5.2 %RANDOM
Rwork0.1475 ---
obs0.14922 10415 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.216 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å2-0 Å2
2---0.59 Å20 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.36→26.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 400 6 179 585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.011494
X-RAY DIFFRACTIONr_bond_other_d0.0020.02237
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.178762
X-RAY DIFFRACTIONr_angle_other_deg1.6263570
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_restr0.090.268
X-RAY DIFFRACTIONr_gen_planes_refined0.0360.02254
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02100
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_it1.0080.892494
X-RAY DIFFRACTIONr_scbond_other1.0050.892493
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4361.348761
X-RAY DIFFRACTIONr_long_range_B_refined4.10710.586737
X-RAY DIFFRACTIONr_long_range_B_other3.6288.981682
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.364→1.399 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 40 -
Rwork0.202 743 -
obs--98.61 %

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