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- PDB-5gsk: Crystal structure of duplex DNA3 in complex with Hg(II) and Sr(II) -

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Basic information

Entry
Database: PDB / ID: 5gsk
TitleCrystal structure of duplex DNA3 in complex with Hg(II) and Sr(II)
ComponentsDNA (5'-D(*GP*GP*TP*CP*GP*TP*CP*C)-3')
KeywordsDNA / metallo-base pair / T-Hg(II)-T
Function / homology: / STRONTIUM ION / DNA
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.05 Å
AuthorsLiu, H.H. / Wang, R. / Yao, Q.Q. / Cheng, Y.Q. / Yang, C. / Luo, Q. / Wu, B.X. / Li, J.X. / Ma, J.B. / Sheng, J. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370728 China
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Flexibility and stabilization of HgII-mediated C:T and T:T base pairs in DNA duplex
Authors: Liu, H.H. / Cai, C. / Haruehanroengra, P. / Yao, Q.Q. / Chen, Y.Q. / Yang, C. / Luo, Q. / Wu, B.X. / Li, J.X. / Ma, J.B. / Sheng, J. / Gan, J.H.
History
DepositionAug 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.3Mar 20, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*TP*CP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,7073
Polymers2,4191
Non-polymers2882
Water79344
1
A: DNA (5'-D(*GP*GP*TP*CP*GP*TP*CP*C)-3')
hetero molecules

A: DNA (5'-D(*GP*GP*TP*CP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,4146
Polymers4,8372
Non-polymers5764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1790 Å2
ΔGint-157 kcal/mol
Surface area2670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.318, 40.318, 24.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-240-

HOH

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Components

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


Mass: 2418.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% v/v MPD, 40 mM Sodium cacodylate, 12 mM Spermine tetra-HCl, 40 mM LiCl, 80 mM SrCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97928 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 1.05→30 Å / Num. obs: 9769 / % possible obs: 96.4 % / Redundancy: 6.9 % / Net I/σ(I): 16.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.05→18.8 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.098 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.025 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15577 444 4.7 %RANDOM
Rwork0.14038 ---
obs0.14374 8921 93.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.342 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.26 Å20 Å2
3----0.52 Å2
Refinement stepCycle: 1 / Resolution: 1.05→18.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 160 2 44 206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.011178
X-RAY DIFFRACTIONr_bond_other_d0.0040.0291
X-RAY DIFFRACTIONr_angle_refined_deg0.8391.163273
X-RAY DIFFRACTIONr_angle_other_deg1.3793215
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_restr0.0520.224
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0293
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0238
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_restr1.1843269
X-RAY DIFFRACTIONr_sphericity_free59.82453
X-RAY DIFFRACTIONr_sphericity_bonded9.6415294
LS refinement shellResolution: 1.051→1.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 17 -
Rwork0.293 411 -
obs--59.78 %

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