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- PDB-5e36: Crystal structure of 2'-propargyl-modified DNA 8mer-duplex -

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Basic information

Entry
Database: PDB / ID: 5.0E+36
TitleCrystal structure of 2'-propargyl-modified DNA 8mer-duplex
ComponentsDNA (5'-D(*GP*(OMU)P*GP*TP*(5JO)P*CP*AP*C)-3')
KeywordsDNA / Modified DNA / 2'-propargyl
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSheng, J. / Gan, J.
CitationJournal: To Be Published
Title: Crystal structure of 2'-propargyl-modified DNA 8mer-duplex
Authors: Sheng, J. / Gan, J.
History
DepositionOct 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_polymer_linkage / 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.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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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*(OMU)P*GP*TP*(5JO)P*CP*AP*C)-3')
B: DNA (5'-D(*GP*(OMU)P*GP*TP*(5JO)P*CP*AP*C)-3')
C: DNA (5'-D(*GP*(OMU)P*GP*TP*(5JO)P*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5395
Polymers7,4903
Non-polymers492
Water3,675204
1
A: DNA (5'-D(*GP*(OMU)P*GP*TP*(5JO)P*CP*AP*C)-3')
B: DNA (5'-D(*GP*(OMU)P*GP*TP*(5JO)P*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0424
Polymers4,9932
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-4 kcal/mol
Surface area3220 Å2
MethodPISA
2
C: DNA (5'-D(*GP*(OMU)P*GP*TP*(5JO)P*CP*AP*C)-3')

C: DNA (5'-D(*GP*(OMU)P*GP*TP*(5JO)P*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,9932
Polymers4,9932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area740 Å2
ΔGint-4 kcal/mol
Surface area3200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.032, 55.526, 75.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-101-

MG

21B-241-

HOH

31C-144-

HOH

41C-167-

HOH

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Components

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


Mass: 2496.664 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% 2-methyl-2,4-pentanediol (MPD), 40 mMsodiumcacodylate(pH 7.0), 12 mMspermine tetra-HCl, 40 mMLiCl, 80 mMstrontium chloride and 20 mM magnesium chloride.

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2014
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.323
111/2H+1/2K, 3/2H-1/2K, -L20.383
11-1/2H+1/2K, 3/2H+1/2K, -L30.293
ReflectionResolution: 1.6→30 Å / Num. obs: 9231 / % possible obs: 98.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 30.94
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 6.96 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z7I

1z7i


Resolution: 1.6→27.76 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.398 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16118 457 5 %RANDOM
Rwork0.1372 ---
obs0.13835 8752 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.874 Å2
Baniso -1Baniso -2Baniso -3
1--3.27 Å2-0 Å20 Å2
2--5.71 Å2-0 Å2
3----2.44 Å2
Refinement stepCycle: 1 / Resolution: 1.6→27.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 498 2 204 704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.012555
X-RAY DIFFRACTIONr_bond_other_d0.0020.02267
X-RAY DIFFRACTIONr_angle_refined_deg1.651.393846
X-RAY DIFFRACTIONr_angle_other_deg2.6053630
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_restr0.4570.281
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02114
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_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.594→1.635 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.156 30 -
Rwork0.158 582 -
obs--91.34 %

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