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- PDB-8ayg: Crystal structure of an intramolecular i-motif at the insulin-lin... -

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Basic information

Entry
Database: PDB / ID: 8ayg
TitleCrystal structure of an intramolecular i-motif at the insulin-linked polymorphic region (ILPR)
ComponentsInsulin-linked polymorphic region, ILPR DNA (31-MER)
KeywordsDNA / i-motif / promoter / insulin-linked polymorphic region
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsParkinson, G.N. / Alexandrou, E. / Waller, Z.A.E. / El-Omari, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privategrand code: 565921, award:177365 United Kingdom
CitationJournal: Nat Commun / Year: 2024
Title: Structural insights into i-motif DNA structures in sequences from the insulin-linked polymorphic region.
Authors: Guneri, D. / Alexandrou, E. / El Omari, K. / Dvorakova, Z. / Chikhale, R.V. / Pike, D.T.S. / Waudby, C.A. / Morris, C.J. / Haider, S. / Parkinson, G.N. / Waller, Z.A.E.
History
DepositionSep 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / citation_author
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.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin-linked polymorphic region, ILPR DNA (31-MER)
B: Insulin-linked polymorphic region, ILPR DNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)18,3562
Polymers18,3562
Non-polymers00
Water39622
1
A: Insulin-linked polymorphic region, ILPR DNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)9,1781
Polymers9,1781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Insulin-linked polymorphic region, ILPR DNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)9,1781
Polymers9,1781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.415, 51.513, 69.847
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: DNA chain Insulin-linked polymorphic region, ILPR DNA (31-MER)


Mass: 9177.918 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.32 Å3/Da / Density % sol: 47.06 % / Description: pseudo-hexagonal
Crystal growTemperature: 283.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2-Methyl-2,4-pentanediol (MPD), sodium chloride, sodium cacodylate, spermine (tetrachloride)
PH range: 5.5 - 6.4 / Temp details: crystals can also be formed at 277.15K

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Data collection

DiffractionMean temperature: 75 K / Ambient temp details: in vacuum (I23) / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.4797 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 2, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.4797 Å / Relative weight: 1
ReflectionResolution: 2.25→47.42 Å / Num. obs: 8133 / % possible obs: 95.2 % / Redundancy: 44.5 % / Biso Wilson estimate: 76.91 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.024 / Rrim(I) all: 0.169 / Net I/σ(I): 30.4 / Num. measured all: 362297 / Scaling rejects: 17192
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.25-2.3222.71.966148866570.7480.4172.0141.788
9-47.4243.80.12474481700.9970.0190.12566.299.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.7data scaling
SHELXphasing
PDB_EXTRACT3.27data extraction
xia2.multiplexdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.25→41.46 Å / SU ML: 0.5215 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 45.592
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2948 423 5.32 %RANDOM
Rwork0.2487 7534 --
obs0.2513 7957 93.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.06 Å2
Refinement stepCycle: LAST / Resolution: 2.25→41.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1212 0 22 1234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01321348
X-RAY DIFFRACTIONf_angle_d1.11262062
X-RAY DIFFRACTIONf_chiral_restr0.0614246
X-RAY DIFFRACTIONf_plane_restr0.007362
X-RAY DIFFRACTIONf_dihedral_angle_d31.8235612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.580.46221480.37482331X-RAY DIFFRACTION89.08
2.58-3.240.46111260.38142434X-RAY DIFFRACTION91.27
3.25-41.460.25121490.21792769X-RAY DIFFRACTION98.78

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