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

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Basic information

Entry
Database: PDB / ID: 5wsr
TitleCrystal structure of T-Hg-T pair containing DNA duplex
ComponentsDNA (5'-D(*GP*GP*TP*CP*GP*TP*CP*C)-3')
KeywordsDNA / DNA duplex / T-Hg-T pair
Function / homology: / DNA
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 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 / 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_atom_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_atom_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.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_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)2,6192
Polymers2,4191
Non-polymers2011
Water93752
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)5,2384
Polymers4,8372
Non-polymers4012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1140 Å2
ΔGint-65 kcal/mol
Surface area2900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.524, 42.524, 25.027
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 / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 47.41 %
Crystal growTemperature: 291 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: Oct 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 3784 / % possible obs: 95 % / Redundancy: 20.6 % / Net I/σ(I): 17.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→21.569 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 12.32
RfactorNum. reflection% reflection
Rfree0.1878 215 5.68 %
Rwork0.168 --
obs0.1691 3784 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→21.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 160 1 52 213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006178
X-RAY DIFFRACTIONf_angle_d0.586273
X-RAY DIFFRACTIONf_dihedral_angle_d12.33776
X-RAY DIFFRACTIONf_chiral_restr0.02431
X-RAY DIFFRACTIONf_plane_restr0.0038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4996-1.88920.25241130.15591730X-RAY DIFFRACTION95
1.8892-21.5710.16771020.17211839X-RAY DIFFRACTION95

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