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Basic information

Entry
Database: PDB / ID: 6iue
TitleDNA helical wire containing Hg(II)
ComponentsDNA (5'-D(*TP*TP*TP*GP*C)-3')
KeywordsDNA / nanowire / mercury / metallo-base pair
Function / homology: / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å
AuthorsOno, A. / Kanazawa, H. / Ito, H. / Goto, M. / Nakamura, K. / Saneyoshi, H. / Kondo, J.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H03033 Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: A Novel DNA Helical Wire Containing HgII-Mediated T:T and T:G Pairs.
Authors: Ono, A. / Kanazawa, H. / Ito, H. / Goto, M. / Nakamura, K. / Saneyoshi, H. / Kondo, J.
History
DepositionNov 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*TP*TP*TP*GP*C)-3')
M: DNA (5'-D(*TP*TP*TP*GP*C)-3')
B: DNA (5'-D(*TP*TP*TP*GP*C)-3')
N: DNA (5'-D(*TP*TP*TP*GP*C)-3')
C: DNA (5'-D(*TP*TP*TP*GP*C)-3')
O: DNA (5'-D(*TP*TP*TP*GP*C)-3')
D: DNA (5'-D(*TP*TP*TP*GP*C)-3')
P: DNA (5'-D(*TP*TP*TP*GP*C)-3')
E: DNA (5'-D(*TP*TP*TP*GP*C)-3')
Q: DNA (5'-D(*TP*TP*TP*GP*C)-3')
F: DNA (5'-D(*TP*TP*TP*GP*C)-3')
R: DNA (5'-D(*TP*TP*TP*GP*C)-3')
G: DNA (5'-D(*TP*TP*TP*GP*C)-3')
T: DNA (5'-D(*TP*TP*TP*GP*C)-3')
H: DNA (5'-D(*TP*TP*TP*GP*C)-3')
U: DNA (5'-D(*TP*TP*TP*GP*C)-3')
I: DNA (5'-D(*TP*TP*TP*GP*C)-3')
V: DNA (5'-D(*TP*TP*TP*GP*C)-3')
J: DNA (5'-D(*TP*TP*TP*GP*C)-3')
W: DNA (5'-D(*TP*TP*TP*GP*C)-3')
K: DNA (5'-D(*TP*TP*TP*GP*C)-3')
X: DNA (5'-D(*TP*TP*TP*GP*C)-3')
L: DNA (5'-D(*TP*TP*TP*GP*C)-3')
Y: DNA (5'-D(*TP*TP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,29372
Polymers35,66424
Non-polymers9,62848
Water1,49583
1
A: DNA (5'-D(*TP*TP*TP*GP*C)-3')
M: DNA (5'-D(*TP*TP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7746
Polymers2,9722
Non-polymers8024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-31 kcal/mol
Surface area2060 Å2
MethodPISA
2
B: DNA (5'-D(*TP*TP*TP*GP*C)-3')
N: DNA (5'-D(*TP*TP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7746
Polymers2,9722
Non-polymers8024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-33 kcal/mol
Surface area2040 Å2
MethodPISA
3
C: DNA (5'-D(*TP*TP*TP*GP*C)-3')
O: DNA (5'-D(*TP*TP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7746
Polymers2,9722
Non-polymers8024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-33 kcal/mol
Surface area2180 Å2
MethodPISA
4
D: DNA (5'-D(*TP*TP*TP*GP*C)-3')
P: DNA (5'-D(*TP*TP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7746
Polymers2,9722
Non-polymers8024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-33 kcal/mol
Surface area2180 Å2
MethodPISA
5
E: DNA (5'-D(*TP*TP*TP*GP*C)-3')
Q: DNA (5'-D(*TP*TP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7746
Polymers2,9722
Non-polymers8024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-32 kcal/mol
Surface area2020 Å2
MethodPISA
6
F: DNA (5'-D(*TP*TP*TP*GP*C)-3')
R: DNA (5'-D(*TP*TP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7746
Polymers2,9722
Non-polymers8024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-31 kcal/mol
Surface area1870 Å2
MethodPISA
7
G: DNA (5'-D(*TP*TP*TP*GP*C)-3')
T: DNA (5'-D(*TP*TP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7746
Polymers2,9722
Non-polymers8024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-32 kcal/mol
Surface area2060 Å2
MethodPISA
8
H: DNA (5'-D(*TP*TP*TP*GP*C)-3')
U: DNA (5'-D(*TP*TP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7746
Polymers2,9722
Non-polymers8024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-31 kcal/mol
Surface area2070 Å2
MethodPISA
9
I: DNA (5'-D(*TP*TP*TP*GP*C)-3')
V: DNA (5'-D(*TP*TP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7746
Polymers2,9722
Non-polymers8024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-31 kcal/mol
Surface area2130 Å2
MethodPISA
10
J: DNA (5'-D(*TP*TP*TP*GP*C)-3')
W: DNA (5'-D(*TP*TP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7746
Polymers2,9722
Non-polymers8024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-31 kcal/mol
Surface area2050 Å2
MethodPISA
11
K: DNA (5'-D(*TP*TP*TP*GP*C)-3')
X: DNA (5'-D(*TP*TP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7746
Polymers2,9722
Non-polymers8024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-30 kcal/mol
Surface area2100 Å2
MethodPISA
12
L: DNA (5'-D(*TP*TP*TP*GP*C)-3')
Y: DNA (5'-D(*TP*TP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7746
Polymers2,9722
Non-polymers8024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-31 kcal/mol
Surface area1880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.929, 28.215, 88.844
Angle α, β, γ (deg.)90.000, 94.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 1486.009 Da / Num. of mol.: 24 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical...
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Hg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: mercury perchlorate, MOPS, spermine, nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.0082 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0082 Å / Relative weight: 1
ReflectionResolution: 1.9→47.621 Å / Num. obs: 41662 / % possible obs: 91.3 % / Redundancy: 1.767 % / Biso Wilson estimate: 8.8 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.126 / Χ2: 2.785 / Net I/σ(I): 8.98
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.951.7780.3284.529760.8650.46388.4
1.95-21.7640.324.4728680.8680.45286.7
2-2.061.7440.2714.6528440.9060.38389.4
2.06-2.131.6610.2295.0627610.9410.32389.1
2.13-2.21.730.2075.5626890.9370.29388.6
2.2-2.271.7960.176.5127020.9570.2493.8
2.27-2.361.8340.1477.3326640.970.20792.3
2.36-2.451.8160.1168.1925320.9780.16495.9
2.45-2.561.7860.0979.1424500.9810.13692.8
2.56-2.691.7160.0839.7622760.9850.11694.5
2.69-2.831.7110.06610.3722750.9920.09394.7
2.83-3.011.8070.05911.3921190.9940.08495.2
3.01-3.211.8310.0512.8318950.9950.0791.6
3.21-3.471.8090.04114.217970.9960.05890.9
3.47-3.81.7280.03814.2115770.9970.05389.6
3.8-4.251.7010.03515.3515140.9970.0592.1
4.25-4.911.8630.03516.2913060.9960.04991
4.91-6.011.8370.03614.6810830.9960.05190
6.01-8.51.6560.03316.078660.9960.04792.9
8.5-47.6211.8610.03219.324680.9940.04590.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
Sir2014phasing
PHASERphasing
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.901→47.621 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 42.62
RfactorNum. reflection% reflection
Rfree0.3463 3913 9.43 %
Rwork0.2936 --
obs0.2985 41496 90.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.91 Å2 / Biso mean: 13.68 Å2 / Biso min: 0.91 Å2
Refinement stepCycle: final / Resolution: 1.901→47.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2314 48 83 2445
Biso mean--28.24 11.97 -
Num. residues----118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112550
X-RAY DIFFRACTIONf_angle_d1.1983896
X-RAY DIFFRACTIONf_chiral_restr0.056448
X-RAY DIFFRACTIONf_plane_restr0.008118
X-RAY DIFFRACTIONf_dihedral_angle_d30.5911084
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9008-1.9240.38621530.3921198135185
1.924-1.94830.37631450.35031354149990
1.9483-1.9740.44411480.37431258140688
1.974-2.0010.40151490.36261294144385
2.001-2.02960.36741420.35411258140087
2.0296-2.05990.40681550.35661343149892
2.0599-2.09210.39131840.32471232141689
2.0921-2.12640.37171450.3291304144988
2.1264-2.1630.32561450.32751318146387
2.163-2.20240.39661270.33551334146191
2.2024-2.24470.39531140.28621359147392
2.2447-2.29050.34041340.28711451158595
2.2905-2.34030.35161400.28451380152093
2.3403-2.39480.32891530.27461353150694
2.3948-2.45470.3721650.27261379154495
2.4547-2.5210.27621290.27071402153194
2.521-2.59520.3341220.25611402152492
2.5952-2.6790.29991350.25631378151395
2.679-2.77470.32371090.25891463157295
2.7747-2.88580.26151420.27991379152194
2.8858-3.01710.31741550.28491371152695
3.0171-3.17610.33311400.26761372151290
3.1761-3.37510.31631280.28851276140489
3.3751-3.63560.32971430.28441339148290
3.6356-4.00130.38761410.25511363150491
4.0013-4.57990.38771270.27581376150392
4.5799-5.76860.32431340.32191309144389
5.7686-47.6360.28991090.2591338144789

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