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- PDB-4l24: Crystal structure of metallo-DNA duplex containing consecutive T-... -

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Basic information

Entry
Database: PDB / ID: 4l24
TitleCrystal structure of metallo-DNA duplex containing consecutive T-Hg(II)-T base pairs
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*TP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / metallo-DNA duplex / B-form DNA duplex / T-Hg(II)-T base pair / B-form double helix / Hg(II)
Function / homology: / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKondo, J. / Yamada, T. / Hirose, C. / Okamoto, I. / Tanaka, Y. / Ono, A.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs
Authors: Kondo, J. / Yamada, T. / Hirose, C. / Okamoto, I. / Tanaka, Y. / Ono, A.
History
DepositionJun 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_site
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_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _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_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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*TP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*TP*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7104
Polymers7,3092
Non-polymers4012
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-67 kcal/mol
Surface area4300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.500, 41.270, 64.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3654.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 47.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium Cacodylate, Spermine tetrahydrochloride, 2-methyl-2,4-pentanediol, ammonium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorDate: Oct 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→34.8 Å / Num. obs: 2064

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BNA

1bna


Resolution: 2.7→34.77 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.267 187 9 %
Rwork0.258 --
obs-2064 99.2 %
Solvent computationBsol: 42.01 Å2
Displacement parametersBiso max: 185.36 Å2 / Biso mean: 62.5829 Å2 / Biso min: 10.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.457 Å20 Å20 Å2
2--37.106 Å20 Å2
3----35.65 Å2
Refinement stepCycle: LAST / Resolution: 2.7→34.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 484 2 14 500
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it21.1542
X-RAY DIFFRACTIONc_mcangle_it20.2152
X-RAY DIFFRACTIONc_scangle_it20.3812.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.80.8869170.8166180197100
2.8-2.910.011130.8338187200100
2.91-3.040.011160.5406180196100
3.04-3.20.011160.3212198214100
3.2-3.40.011120.2879178190100
3.4-3.660.011240.1891195219100
3.66-4.030.011140.2313189203100
4.03-4.620.011230.2189184207100
4.62-5.820.011250.2334192217100
5.82-1000.011270.260219422193.2
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna-rna_free.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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