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- PDB-9mxo: Motif2-Motif1 Left-handed parallel G-quadruplex in H3 Spacegroup -

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Basic information

Entry
Database: PDB / ID: 9mxo
TitleMotif2-Motif1 Left-handed parallel G-quadruplex in H3 Spacegroup
ComponentsDNA (26-MER)
KeywordsDNA / G-quadruplex / left-handed G-quadruplex / parallel / Motif2-Motif1
Function / homology: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / SPERMINE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsHendrickson, A.D. / Xing, E.R. / 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: Preservation of left-handed fold and interaction with N-methylmesoporphyrin IX by two-block sequences with left-hand folding potential
Authors: Hendrickson, A.D. / Xing, E.R. / Yatsunyk, L.A.
History
DepositionJan 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: 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 (26-MER)
B: DNA (26-MER)
C: DNA (26-MER)
D: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,72623
Polymers33,0574
Non-polymers1,66919
Water2,522140
1
A: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3824
Polymers8,2641
Non-polymers1173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8927
Polymers8,2641
Non-polymers6286
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9207
Polymers8,2641
Non-polymers6566
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5325
Polymers8,2641
Non-polymers2674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.649, 104.649, 65.365
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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DNA chain , 1 types, 4 molecules ABCD

#1: DNA chain
DNA (26-MER)


Mass: 8264.264 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 159 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 42.3 % / Description: Very long, thin rods
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05 M Potassium chloride, 0.005 M Spermine tetrahydrochloride, 0.05 M Bis-Tris 7.0, 33% w/v PEG 4000

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Data collection

DiffractionMean temperature: 196 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920119 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920119 Å / Relative weight: 1
ReflectionResolution: 1.68→30.341 Å / Num. obs: 29303 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 30.17 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.13 / Net I/σ(I): 8.6
Reflection shellResolution: 1.682→1.711 Å / Redundancy: 8.6 % / Rmerge(I) obs: 4.45 / Num. unique obs: 1636 / CC1/2: 0.414 / Rrim(I) all: 5.068 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.21.2_5419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→30.34 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2021 1661 5.67 %
Rwork0.1719 --
obs0.1736 29303 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→30.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2196 93 140 2429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082538
X-RAY DIFFRACTIONf_angle_d1.0233891
X-RAY DIFFRACTIONf_dihedral_angle_d38.0581084
X-RAY DIFFRACTIONf_chiral_restr0.05412
X-RAY DIFFRACTIONf_plane_restr0.01104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.730.3575910.34831545X-RAY DIFFRACTION65
1.73-1.790.4071590.34252266X-RAY DIFFRACTION96
1.79-1.850.34731320.30672363X-RAY DIFFRACTION99
1.85-1.930.34761290.29082420X-RAY DIFFRACTION100
1.93-2.010.28491590.27292374X-RAY DIFFRACTION100
2.01-2.120.30361520.23912370X-RAY DIFFRACTION100
2.12-2.250.27141440.23652373X-RAY DIFFRACTION100
2.25-2.430.24191460.2112382X-RAY DIFFRACTION100
2.43-2.670.24421110.20772420X-RAY DIFFRACTION100
2.67-3.060.22911570.1832358X-RAY DIFFRACTION100
3.06-3.850.16851500.14292386X-RAY DIFFRACTION100
3.85-30.340.11841310.10422385X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.96-0.03260.31597.2041.87486.50950.02160.4540.9391-0.86590.1218-0.1586-0.5695-0.1482-0.14020.3486-0.00670.08950.3030.15750.4236-1.7028-36.8765-23.7443
22.6392-4.08361.53776.5739-2.03081.220.13810.00510.3713-0.42690.0275-0.4688-0.11060.1605-0.12360.30910.0670.11530.31150.08320.3926.2197-43.7577-17.8828
37.41781.48580.45636.59050.18585.145-0.02920.41680.6639-0.3230.06740.36160.0211-0.3075-0.02760.2515-0.00410.02120.26460.07670.3569-6.7153-40.7107-18.2127
46.3385-2.4367-1.1629.15884.49066.88860.0036-0.6791-0.72910.21640.2693-0.02470.31380.2074-0.2780.19330.0038-0.01320.38460.06520.3061.6583-22.081-26.2438
53.8887-0.07612.71151.6373-1.17776.0083-0.0204-0.0095-0.8069-0.20180.12980.49550.0058-0.4128-0.02850.2873-0.0244-0.05310.3372-0.00040.4899-6.7245-19.5899-34.6048
67.7496-3.224-0.73468.3933-0.79943.52360.0447-0.2621-0.2363-0.04060.1852-0.35870.00110.2778-0.2140.1945-0.0377-0.00530.2891-0.05220.33586.3013-18.5429-32.3357
77.7473-0.76241.72939.3501-0.01397.0868-0.0125-0.82260.51170.972-0.1749-0.280.27520.16120.17580.4138-0.0216-0.01750.35-0.11460.306210.4452-38.9314-37.4864
84.23461.49193.89734.9696-0.80646.5730.2867-0.5940.26750.9298-0.40581.47280.3298-0.96550.0580.4427-0.1280.12860.412-0.14040.46830.4771-42.2589-43.5569
99.5433-1.26141.38178.1836-0.79197.59690.0667-0.46740.29890.4962-0.1029-0.75910.4480.23030.08320.37430.0095-0.0480.2615-0.04180.216213.611-44.4357-43.0149
109.08790.4933-0.92758.81681.48527.01020.0110.59271.5625-0.2713-0.06061.0193-0.3773-0.25850.09850.257-0.0547-0.04980.33880.00610.5599-12.4575-41.8442-56.9748
119.18897.3279-6.84777.4073-6.49675.7780.1597-0.52321.1097-0.14090.1930.8591-0.4147-0.2011-0.39520.2996-0.01770.01280.4075-0.09140.4003-17.4851-48.8821-48.3153
124.9476-0.92250.49856.54910.99297.17240.1756-0.25591.09870.1951-0.06470.3344-0.2220.2061-0.13060.2544-0.07080.02270.3063-0.12790.5545-6.6094-41.6766-50.8431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 15 )
3X-RAY DIFFRACTION3chain 'A' and (resid 16 through 26 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 10 )
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 15 )
6X-RAY DIFFRACTION6chain 'B' and (resid 16 through 26 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 10 )
8X-RAY DIFFRACTION8chain 'C' and (resid 11 through 15 )
9X-RAY DIFFRACTION9chain 'C' and (resid 16 through 26 )
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 10 )
11X-RAY DIFFRACTION11chain 'D' and (resid 11 through 15 )
12X-RAY DIFFRACTION12chain 'D' and (resid 16 through 26 )

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