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- PDB-5wsq: Crystal structure of C-Hg-T pair containing DNA duplex -

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Basic information

Entry
Database: PDB / ID: 5wsq
TitleCrystal structure of C-Hg-T pair containing DNA duplex
ComponentsDNA (5'-D(*GP*CP*CP*CP*GP*TP*GP*C)-3')
KeywordsDNA / DNA duplex / C-Hg-T pair
Function / homology: / 1,3-PROPANDIOL / DNA
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.05 Å
AuthorsGan, J.H. / Liu, H.H.
Funding support China, 2items
OrganizationGrant numberCountry
the Key Research and Development Project of China2016YFA0500600 China
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
DepositionDec 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,2845
Polymers4,8072
Non-polymers4773
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-61 kcal/mol
Surface area2840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.848, 51.138, 21.593
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 2403.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-PDO / 1,3-PROPANDIOL / 1,3-Propanediol


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 10% v/v MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.05→30 Å / Num. obs: 19098 / % possible obs: 98.1 % / Redundancy: 2 % / Rsym value: 0.12 / Net I/σ(I): 24
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 1.9 % / CC1/2: 0.653 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.05→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.027 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17491 1023 5.1 %RANDOM
Rwork0.15521 ---
obs0.1562 19098 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.289 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 318 7 62 387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.011358
X-RAY DIFFRACTIONr_bond_other_d0.0010.02184
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.172545
X-RAY DIFFRACTIONr_angle_other_deg2.0623432
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_restr0.0710.248
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02188
X-RAY DIFFRACTIONr_gen_planes_other0.0130.0284
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_it0.6671.28357
X-RAY DIFFRACTIONr_scbond_other0.6641.279356
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8911.93546
X-RAY DIFFRACTIONr_long_range_B_refined1.23713.242534
X-RAY DIFFRACTIONr_long_range_B_other1.23613.244535
X-RAY DIFFRACTIONr_rigid_bond_restr2.5663541
X-RAY DIFFRACTIONr_sphericity_free13.12512
X-RAY DIFFRACTIONr_sphericity_bonded4.245559
LS refinement shellResolution: 1.051→1.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 73 -
Rwork0.271 1398 -
obs--99.26 %

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