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- PDB-7jlh: Structure of Centromeric Satellite III Non-canonical Duplex -

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Basic information

Entry
Database: PDB / ID: 7jlh
TitleStructure of Centromeric Satellite III Non-canonical Duplex
ComponentsDNA AATGG
KeywordsDNA / non-canonical DNA / duplex / fiber / Satellite III
Function / homologyACETATE ION / DNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsYatsunyk, L.A. / Chen, E.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA208676-01A1 United States
CitationJournal: To Be Published
Title: Crystal Structure of 4-repeat Satellite III Sequence with Non-Canonical Base Interactions
Authors: Yatsunyk, L.A. / Chen, E.V. / Lee, H.
History
DepositionJul 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA AATGG
B: DNA AATGG
C: DNA AATGG
D: DNA AATGG
E: DNA AATGG
F: DNA AATGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3488
Polymers9,2646
Non-polymers832
Water1,33374
1
A: DNA AATGG
B: DNA AATGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,1714
Polymers3,0882
Non-polymers832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA AATGG
D: DNA AATGG


Theoretical massNumber of molelcules
Total (without water)3,0882
Polymers3,0882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DNA AATGG
F: DNA AATGG


Theoretical massNumber of molelcules
Total (without water)3,0882
Polymers3,0882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.522, 40.217, 55.379
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: DNA chain
DNA AATGG


Mass: 1544.061 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: DNA consists of four ATGGA repeats. Packing of DNA into crystal structure leads to the presence of three antiparallel AATGG duplexes in the asymmetric unit.
Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThe full DNA sequence is d(ATGGA)4 which forms self complimentary duplex. Due to the repetitive ...The full DNA sequence is d(ATGGA)4 which forms self complimentary duplex. Due to the repetitive nature and symmetry of such duplex, the asymmetric unit only includes 1/4 of the duplex, with the sequences AATGG. There are three such duplexes in the ASU.

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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: 2.19 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Tris-Acetate, potassium acetate, magnesium acetate, MES monohydrate, 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 196 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.0711 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2019
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0711 Å / Relative weight: 1
ReflectionResolution: 1.57→32.54 Å / Num. obs: 12855 / % possible obs: 99.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 31.32 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.1
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 643 / CC1/2: 0.991 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSJan 31, 2020data scaling
pointlessv7.1.002data scaling
Aimlessv7.1.002data scaling
PHASER1.18_3845phasing
Cootv0.8.9.2model building
XDSJan 31, 2020data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 175D

175d


Resolution: 1.57→32.54 Å / SU ML: 0.2088 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.2896
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2551 1257 9.93 %
Rwork0.2206 11402 -
obs0.224 12659 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.43 Å2
Refinement stepCycle: LAST / Resolution: 1.57→32.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 636 5 74 715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017717
X-RAY DIFFRACTIONf_angle_d1.6681095
X-RAY DIFFRACTIONf_chiral_restr0.1189120
X-RAY DIFFRACTIONf_plane_restr0.016631
X-RAY DIFFRACTIONf_dihedral_angle_d33.668282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.630.37851290.30421226X-RAY DIFFRACTION95.69
1.63-1.710.29661330.27081188X-RAY DIFFRACTION94.7
1.71-1.80.30251440.25421233X-RAY DIFFRACTION98.15
1.8-1.910.3141360.25351247X-RAY DIFFRACTION99.14
1.91-2.060.30961430.2611266X-RAY DIFFRACTION99.51
2.06-2.260.28271410.25771276X-RAY DIFFRACTION99.86
2.26-2.590.34041390.26781282X-RAY DIFFRACTION99.79
2.59-3.260.24681440.24071307X-RAY DIFFRACTION99.59
3.26-32.540.21771480.18251377X-RAY DIFFRACTION99.48
Refinement TLS params.Method: refined / Origin x: 0.832115918806 Å / Origin y: -19.1431532399 Å / Origin z: -3.07229969381 Å
111213212223313233
T0.170302751642 Å20.00521666156345 Å2-0.0236401051334 Å2-0.350078478293 Å20.040265444824 Å2--0.359974141002 Å2
L3.88126699329 °2-0.938888015653 °20.101154490172 °2-3.55499803258 °20.0377720632787 °2--3.3709083206 °2
S0.0897456756304 Å °-0.571024576797 Å °-0.558741408613 Å °0.1074646575 Å °0.0595539543837 Å °-0.056717361214 Å °0.0212668735776 Å °0.213822502467 Å °-0.160687112359 Å °
Refinement TLS groupSelection details: all

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