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- PDB-5ix7: Crystal structure of metallo-DNA nanowire with infinite one-dimen... -

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Basic information

Entry
Database: PDB / ID: 5ix7
TitleCrystal structure of metallo-DNA nanowire with infinite one-dimensional silver array
ComponentsDNA (5'-D(*GP*GP*AP*CP*TP*(CBR)P*GP*AP*CP*TP*CP*C)-3')
KeywordsDNA / nanowire / X-ray analysis / metallo-base pairs / silver
Function / homologySILVER ION / : / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.398 Å
AuthorsKondo, J. / Tada, Y. / Dairaku, T. / Hattori, Y. / Saneyoshi, H. / Ono, A. / Tanaka, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
MEXT24245037 Japan
MEXTS1201015 Japan
Murata Science Foundation Japan
CitationJournal: Nat Chem / Year: 2017
Title: A metallo-DNA nanowire with uninterrupted one-dimensional silver array
Authors: Kondo, J. / Tada, Y. / Dairaku, T. / Hattori, Y. / Saneyoshi, H. / Ono, A. / Tanaka, Y.
History
DepositionMar 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Mar 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_conn_type
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_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.ptnr1_symmetry / _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_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.ptnr3_symmetry / _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_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_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_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,4289
Polymers3,7021
Non-polymers7258
Water1,58588
1
A: DNA (5'-D(*GP*GP*AP*CP*TP*(CBR)P*GP*AP*CP*TP*CP*C)-3')
hetero molecules

A: DNA (5'-D(*GP*GP*AP*CP*TP*(CBR)P*GP*AP*CP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,85518
Polymers7,4052
Non-polymers1,45116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area5080 Å2
ΔGint-86 kcal/mol
Surface area3570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.150, 30.150, 118.420
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-101-

AG

21A-106-

AG

31A-203-

HOH

41A-219-

HOH

51A-232-

HOH

61A-237-

HOH

71A-239-

HOH

81A-248-

HOH

91A-256-

HOH

101A-261-

HOH

111A-268-

HOH

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Components

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


Mass: 3702.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-AG / SILVER ION / Silver


Mass: 107.868 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ag
#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 / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: MOPS (pH 7.0), Spermine, MPD, KNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.4→26.111 Å / Num. obs: 11942 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.02 % / Biso Wilson estimate: 10.16 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.079 / Χ2: 1.169 / Net I/σ(I): 19.68 / Num. measured all: 119653 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.439.2720.2846.9584109059070.9470.301100
1.43-1.4710.4770.2199.6988018408400.9710.231100
1.47-1.5210.4980.17311.7488718458450.9880.182100
1.52-1.5610.6020.17411.7584928018010.9880.183100
1.56-1.6110.6420.15613.6283437847840.9840.165100
1.61-1.6710.5090.13915.7782817887880.9850.146100
1.67-1.7310.4430.12318.4774987187180.990.129100
1.73-1.810.4220.11319.6374417147140.9930.119100
1.8-1.8810.3480.10421.0370686836830.9930.11100
1.88-1.9810.2230.09722.7164716336330.9940.102100
1.98-2.0810.0830.08624.2662116166160.9950.091100
2.08-2.219.7620.07826.7457015845840.9960.082100
2.21-2.369.4820.07128.2552535545540.9970.076100
2.36-2.559.480.06829.5649205195190.9980.071100
2.55-2.89.3380.06530.4742304534530.9960.068100
2.8-3.139.5620.0631.2640834274270.9980.064100
3.13-3.619.6160.05631.4636353783780.9990.06100
3.61-4.429.1490.04831.3129463223220.9990.051100
4.42-6.257.5020.04429.3318082412410.9990.047100
6.25-26.1118.8150.05432.1711901361350.9930.05899.3

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
XSCALEdata scaling
AutoSolphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.398→26.111 Å / FOM work R set: 0.9069 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 15.73 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.1886 1195 10.01 %
Rwork0.1651 10742 -
obs0.1675 11937 99.95 %
Solvent computationShrinkage radii: 0.05 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.499 Å2 / ksol: 0.542 e/Å3
Displacement parametersBiso max: 57.2 Å2 / Biso mean: 25.09 Å2 / Biso min: 5.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.5821 Å20 Å2-0 Å2
2--0.5821 Å20 Å2
3----1.1643 Å2
Refinement stepCycle: final / Resolution: 1.398→26.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 241 8 88 337
Biso mean--16.46 33.59 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019269
X-RAY DIFFRACTIONf_angle_d1.31411
X-RAY DIFFRACTIONf_chiral_restr0.08846
X-RAY DIFFRACTIONf_plane_restr0.01512
X-RAY DIFFRACTIONf_dihedral_angle_d33.488125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.3976-1.45350.27841660.193911691335
1.4535-1.51970.22481400.187311771317
1.5197-1.59980.22941260.199712031329
1.5998-1.70.23561140.176112201334
1.7-1.83120.20461060.164811871293
1.8312-2.01540.24091270.174112361363
2.0154-2.30690.17681240.152411921316
2.3069-2.90590.1611670.136111561323
2.9059-26.11520.15321250.16912021327

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