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- PDB-5xuv: Crystal structure of DNA duplex containing 4-thiothymine-2Ag(I)-4... -

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Basic information

Entry
Database: PDB / ID: 5xuv
TitleCrystal structure of DNA duplex containing 4-thiothymine-2Ag(I)-4-thiothymine base pairs
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*(8RO)P*(8RO)P*TP*CP*GP*CP*G)-3')
KeywordsDNA / metallo-base pair / silver
Function / homologySILVER ION / : / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsKondo, J. / Sugawara, T. / Saneyoshi, H. / Ono, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
MEXT17H03033 Japan
CitationJournal: Chem. Commun. (Camb.) / Year: 2017
Title: Crystal structure of a DNA duplex containing four Ag(i) ions in consecutive dinuclear Ag(i)-mediated base pairs: 4-thiothymine-2Ag(i)-4-thiothymine
Authors: Kondo, J. / Sugawara, T. / Saneyoshi, H. / Ono, A.
History
DepositionJun 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...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_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_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.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.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.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(*CP*GP*CP*GP*AP*(8RO)P*(8RO)P*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*(8RO)P*(8RO)P*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8198
Polymers7,3092
Non-polymers5106
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-29 kcal/mol
Surface area4040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.213, 40.487, 66.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*GP*AP*(8RO)P*(8RO)P*TP*CP*GP*CP*G)-3')


Mass: 3654.512 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, silver nitrate, spermine, 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→33.216 Å / Num. obs: 10314 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.703 % / Biso Wilson estimate: 31.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.049 / Χ2: 1.315 / Net I/σ(I): 20.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.956.3450.2935.027370.9820.31996.8
1.95-26.4780.2595.737190.9870.281100
2-2.066.440.2286.857320.9870.248100
2.06-2.126.9580.1998.287110.9880.21599.9
2.12-2.197.1210.1410.816760.9970.1599.9
2.19-2.276.8190.11312.56960.9970.123100
2.27-2.3670.09714.886150.9980.104100
2.36-2.456.6450.07317.846050.9990.08100
2.45-2.566.60.07820.186020.9980.084100
2.56-2.696.4840.06822.765640.9980.074100
2.69-2.837.2020.05826.365400.9990.062100
2.83-37.0710.04528.6749510.049100
3-3.216.8630.03633.1748310.03999.6
3.21-3.476.430.04334.684330.9990.04799.5
3.47-3.86.2170.03738.034060.9990.041100
3.8-4.256.5640.03642.233740.9990.04100
4.25-4.96.7420.03542.833290.9990.038100
4.9-6.016.6920.03343.592730.9990.036100
6.01-8.496.0860.03344.542100.9990.036100
8.49-33.2167.3250.02850.351140.9990.0399.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L24

4l24


Resolution: 1.9→33.216 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 23.84
RfactorNum. reflection% reflection
Rfree0.2216 997 9.73 %
Rwork0.1854 --
obs0.189 10250 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.98 Å2 / Biso mean: 41.1742 Å2 / Biso min: 30.96 Å2
Refinement stepCycle: final / Resolution: 1.9→33.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 484 50 23 557
Biso mean--41.7 42.15 -
Num. residues----22
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008540
X-RAY DIFFRACTIONf_angle_d1.088830
X-RAY DIFFRACTIONf_chiral_restr0.04790
X-RAY DIFFRACTIONf_plane_restr0.00724
X-RAY DIFFRACTIONf_dihedral_angle_d34.381208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8988-1.99890.23811300.21421300143098
1.9989-2.12410.20141500.198713271477100
2.1241-2.28810.22931530.19581334148799
2.2881-2.51820.22481340.200113511485100
2.5182-2.88250.26651350.212113351470100
2.8825-3.63090.28041250.21611297142296
3.6309-33.22110.18381700.147213091479100

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