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- PDB-4r6m: Crystal Structure of DNA Duplex Containing Two Consecutive Mercur... -

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Basic information

Entry
Database: PDB / ID: 4r6m
TitleCrystal Structure of DNA Duplex Containing Two Consecutive Mercury-mediated Base Pairs
Components
  • DNA (5'-D(P*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B Double Helix / metallo DNA duplex
Function / homology: / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.357 Å
AuthorsXu, C.Y. / Yu, F. / Wang, L.H. / Zhao, Y. / Lin, T. / Fan, C.H. / He, J.H.
CitationJournal: To be Published
Title: Crystal Structure of DNA Duplex Containing Two Consecutive Mercury-mediated Base Pairs
Authors: Xu, C.Y. / Yu, F. / Wang, L.H. / Zhao, Y. / Lin, T. / Fan, C.H. / He, J.H.
History
DepositionAug 26, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 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 / 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_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,42212
Polymers18,2196
Non-polymers1,2046
Water21612
1
A: DNA (5'-D(P*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(P*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4744
Polymers6,0732
Non-polymers4012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-65 kcal/mol
Surface area3980 Å2
MethodPISA
2
C: DNA (5'-D(P*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3')
D: DNA (5'-D(P*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4744
Polymers6,0732
Non-polymers4012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-65 kcal/mol
Surface area3880 Å2
MethodPISA
3
E: DNA (5'-D(P*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3')
F: DNA (5'-D(P*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4744
Polymers6,0732
Non-polymers4012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-69 kcal/mol
Surface area4010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.785, 70.785, 108.037
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 3061.004 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3')


Mass: 3011.966 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.86 Å3/Da / Density % sol: 56.98 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.75
Details: 0.08 M Potassium Chloride, 0.02 M Magnesium Chloride, 0.012 M Spermine Tetrahydrochloride, 40% 2-methyl-2,4-pentanediol, 0.04 M Sodium cacodylate trihydrate, pH 6.75, VAPOR DIFFUSION, ...Details: 0.08 M Potassium Chloride, 0.02 M Magnesium Chloride, 0.012 M Spermine Tetrahydrochloride, 40% 2-methyl-2,4-pentanediol, 0.04 M Sodium cacodylate trihydrate, pH 6.75, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.00928 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00928 Å / Relative weight: 1
ReflectionResolution: 2.357→36.01 Å / Num. obs: 16444 / % possible obs: 97.64 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.1 % / Rmerge(I) obs: 0.084 / Rsym value: 0.093

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.357→26.658 Å / FOM work R set: 0.7285 / SU ML: 0.36 / σ(F): 1.96 / σ(I): 2 / Phase error: 33.54 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 754 4.64 %RANDOM
Rwork0.2155 ---
obs0.2167 16263 97.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.78 Å2 / Biso mean: 76.86 Å2 / Biso min: 35.48 Å2
Refinement stepCycle: LAST / Resolution: 2.357→26.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1224 6 12 1242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041362
X-RAY DIFFRACTIONf_angle_d0.5852088
X-RAY DIFFRACTIONf_chiral_restr0.024240
X-RAY DIFFRACTIONf_plane_restr0.00260
X-RAY DIFFRACTIONf_dihedral_angle_d33.411582
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3574-2.53920.38481700.34462842301291
2.5392-2.79450.32271300.295731763306100
2.7945-3.19830.32251580.254932023360100
3.1983-4.02730.24651540.216531503304100
4.0273-26.660.18831420.17913139328198

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