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- PDB-8taa: Right-left hybrid parallel G-quadruplex in complex with N-methyl ... -

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Basic information

Entry
Database: PDB / ID: 8taa
TitleRight-left hybrid parallel G-quadruplex in complex with N-methyl mesoporphyrin
ComponentsDNA (25-MER)
KeywordsDNA / G-quadruplex / right-left-handed / parallel / NMM
Function / homology: / N-METHYLMESOPORPHYRIN / SPERMINE / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSeth, P.C. / Yatsunyk, L.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA253134 United States
CitationJournal: To Be Published
Title: Right-left hybrid parallel G-quadruplex in complex with N-methyl mesoporphyrin
Authors: Seth, P.C. / Yatsunyk, L.A.
History
DepositionJun 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9887
Polymers7,9691
Non-polymers1,0196
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.897, 30.897, 141.543
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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DNA chain , 1 types, 1 molecules A

#1: DNA chain DNA (25-MER)


Mass: 7969.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 44 molecules

#2: Chemical ChemComp-MMP / N-METHYLMESOPORPHYRIN


Mass: 580.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H40N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43 % / Description: Amorphous cubes
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2mM Spermine, 45% MPD, 0.08M Nacl, 0.04M NaCaCo pH 6.0

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Data collection

DiffractionMean temperature: 196 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.45→141.54 Å / Num. obs: 13141 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 28.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.015 / Rrim(I) all: 0.051 / Net I/σ(I): 21
Reflection shellResolution: 1.45→1.47 Å / Rmerge(I) obs: 1.789 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 647 / CC1/2: 0.678 / Rpim(I) all: 0.523 / Rrim(I) all: 1.866 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Coot0.8.9.2model building
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→35.39 Å / SU ML: 0.1935 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.5306
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2307 702 5.38 %
Rwork0.2115 12347 -
obs0.2125 13049 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.7 Å2
Refinement stepCycle: LAST / Resolution: 1.45→35.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 530 56 38 624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128651
X-RAY DIFFRACTIONf_angle_d1.72821001
X-RAY DIFFRACTIONf_chiral_restr0.0781100
X-RAY DIFFRACTIONf_plane_restr0.018429
X-RAY DIFFRACTIONf_dihedral_angle_d36.7692258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.560.33061420.30832400X-RAY DIFFRACTION100
1.56-1.720.21281270.22152414X-RAY DIFFRACTION99.73
1.72-1.970.25671370.24212408X-RAY DIFFRACTION99.84
1.97-2.480.23851420.26632471X-RAY DIFFRACTION100
2.48-35.390.22291540.19072654X-RAY DIFFRACTION99.79
Refinement TLS params.Method: refined / Origin x: -3.87659260113 Å / Origin y: 4.04022731035 Å / Origin z: -9.68207529396 Å
111213212223313233
T0.33497269125 Å2-0.0145728138347 Å2-0.0229539036274 Å2-0.162597884683 Å20.0338984785581 Å2--0.231093381555 Å2
L3.36064783628 °2-2.42574079131 °2-1.69324077964 °2-8.45717898314 °22.7075881783 °2--4.83369064181 °2
S0.216497696061 Å °0.0415644526618 Å °0.0938266956623 Å °-0.712289719168 Å °-0.0564351824463 Å °0.155054122983 Å °-0.238970125618 Å °0.0899681661486 Å °-0.154548326487 Å °
Refinement TLS groupSelection details: all

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