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- PDB-5w1z: Crystal Structure of inosine-substituted decamer duplex DNA (I4) -

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Basic information

Entry
Database: PDB / ID: 5w1z
TitleCrystal Structure of inosine-substituted decamer duplex DNA (I4)
ComponentsDNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*(BRU)P*IP*I)-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 / SAD / Resolution: 1.55 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 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation / Item: _citation.page_last
Revision 1.2Oct 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 1.3Mar 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 / struct_conn_type
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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_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.ptnr3_symmetry / _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.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.ptnr1_symmetry / _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 / _struct_conn_type.id

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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*(BRU)P*IP*I)-3')
B: DNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*(BRU)P*IP*I)-3')
C: DNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*(BRU)P*IP*I)-3')
D: DNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*(BRU)P*IP*I)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,36811
Polymers12,2034
Non-polymers1657
Water2,810156
1
A: DNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*(BRU)P*IP*I)-3')
B: DNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*(BRU)P*IP*I)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1494
Polymers6,1022
Non-polymers472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-10 kcal/mol
Surface area3450 Å2
MethodPISA
2
C: DNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*(BRU)P*IP*I)-3')
D: DNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*(BRU)P*IP*I)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2197
Polymers6,1022
Non-polymers1185
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-15 kcal/mol
Surface area3460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.884, 32.798, 34.034
Angle α, β, γ (deg.)90.25, 107.32, 111.04
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain
DNA (5'-D(*CP*CP*AP*IP*IP*CP*CP*(BRU)P*IP*I)-3')


Mass: 3050.807 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.01 Å3/Da / Density % sol: 38.87 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Droplets (2 uL) containing oligonucleotide (0.6 mM), sodium cacodylate (20 mM, pH 6.0), magnesium acetate (12.5 mM), and MPD (20% v/v) that were equilibrated against a 1 mL reservoir of ...Details: Droplets (2 uL) containing oligonucleotide (0.6 mM), sodium cacodylate (20 mM, pH 6.0), magnesium acetate (12.5 mM), and 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)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.55→32.24 Å / Num. obs: 13618 / % possible obs: 97.1 % / Observed criterion σ(I): 5 / Redundancy: 5.9 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.053 / Net I/σ(I): 28.7
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1 / Num. unique obs: 640 / Rpim(I) all: 0.434 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→32.24 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.815 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.102
RfactorNum. reflection% reflectionSelection details
Rfree0.23358 801 5.9 %RANDOM
Rwork0.20696 ---
obs0.20857 12813 94.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.471 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20.37 Å20.73 Å2
2---0.8 Å2-0.14 Å2
3----1.11 Å2
Refinement stepCycle: 1 / Resolution: 1.55→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 792 7 156 955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.012902
X-RAY DIFFRACTIONr_bond_other_d0.0020.02411
X-RAY DIFFRACTIONr_angle_refined_deg2.0851.3251382
X-RAY DIFFRACTIONr_angle_other_deg1.6831003
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_restr0.110.2123
X-RAY DIFFRACTIONr_gen_planes_refined0.0370.02445
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02156
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_it2.7251.956902
X-RAY DIFFRACTIONr_scbond_other2.7261.956901
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6672.9611383
X-RAY DIFFRACTIONr_long_range_B_refined5.91919.6271243
X-RAY DIFFRACTIONr_long_range_B_other5.82518.9181204
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 35 -
Rwork0.316 655 -
obs--63.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2398-0.14790.22130.1301-0.15310.213-0.00060.02760.01790.0293-0.0336-0.0462-0.01280.02860.03430.023-0.0107-0.02470.01690.00950.05518.37316.123812.9851
20.3202-0.1075-0.22290.3837-0.27890.5802-0.00580.0351-0.03130.0105-0.05190.0206-0.0080.01680.05760.0092-0.0027-0.01440.0086-0.00280.054813.492921.9646-4.535
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 10
2X-RAY DIFFRACTION1B11 - 20
3X-RAY DIFFRACTION2C1 - 10
4X-RAY DIFFRACTION2D11 - 20

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