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- PDB-7yvx: Left-handed DNA duplex containing consecutive G-G base pairs -

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Basic information

Entry
Database: PDB / ID: 7yvx
TitleLeft-handed DNA duplex containing consecutive G-G base pairs
ComponentsDNA (5'-D(*CP*GP*(CBR)P*GP*GP*GP*CP*GP*CP*G)-3')
KeywordsDNA / Z-form / DNA nanotechnology
Function / homology: / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsKondo, J.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)21H01956 Japan
CitationJournal: To Be Published
Title: Left-handed DNA duplex containing consecutive G-G base pairs
Authors: Kondo, J.
History
DepositionAug 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,3434
Polymers3,1661
Non-polymers1773
Water00
1
A: DNA (5'-D(*CP*GP*(CBR)P*GP*GP*GP*CP*GP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)6,6858
Polymers6,3322
Non-polymers3546
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2480 Å2
ΔGint-11 kcal/mol
Surface area3480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.375, 43.375, 71.998
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-101-

CO

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Components

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


Mass: 3165.900 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
Has ligand of interestY

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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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: MPD, sodium chloride, hexammine cobalt chloride, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.605 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.605 Å / Relative weight: 1
ReflectionResolution: 2.99→37.56 Å / Num. obs: 1553 / % possible obs: 99.7 % / Redundancy: 10.003 % / Biso Wilson estimate: 54.539 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.106 / Χ2: 1.163 / Net I/σ(I): 18.64
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
3-3.1610.2820.3189.8223342272270.9880.335100
3.16-3.3510.5350.19712.3622862172170.9970.207100
3.35-3.5810.1160.12917.1520031981980.9970.136100
3.58-3.879.3660.10718.0617141831830.9950.114100
3.87-4.248.5920.09920.0914951741740.9950.105100
4.24-4.7410.8220.1122.3616991571570.9950.116100
4.74-5.4710.7330.09524.6114491361350.9950.199.3
5.47-6.710.230.08627.0411561131130.9990.09100
6.7-9.479.9890.07927.2894996950.9980.08399
9.47-37.568.3330.0625.1645056540.9980.06496.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→37.56 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.54 / Phase error: 16.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 149 9.69 %
Rwork0.1953 1389 -
obs0.2007 1538 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.24 Å2 / Biso mean: 50.3472 Å2 / Biso min: 28.95 Å2
Refinement stepCycle: final / Resolution: 2.99→37.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 206 3 0 209
Biso mean--103.14 --
Num. residues----10
LS refinement shellResolution: 2.99→3.16 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.255 149 -
Rwork0.1953 1389 -
all-1538 -
obs--100 %

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