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- PDB-6tqi: I-MOTIF STRUCTURE FORMED FROM THE C STRAND OF A HUMAN TELOMERE FR... -

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Basic information

Entry
Database: PDB / ID: 6tqi
TitleI-MOTIF STRUCTURE FORMED FROM THE C STRAND OF A HUMAN TELOMERE FRAGMENT
ComponentsDNA (5'-*TP*AP*AP*CP*CP*CP*TP*AP*A-3')
KeywordsDNA / telomeric / i-motif
Function / homologyDNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsParkinson, G.N. / Wagner, A. / Viladoms-Claverol, J. / Duman, R. / El-Omari, K.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths.
Authors: Zhang, Y. / El Omari, K. / Duman, R. / Liu, S. / Haider, S. / Wagner, A. / Parkinson, G.N. / Wei, D.
History
DepositionDec 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 11, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 (5'-*TP*AP*AP*CP*CP*CP*TP*AP*A-3')


Theoretical massNumber of molelcules
Total (without water)2,6841
Polymers2,6841
Non-polymers00
Water00
1
A: DNA (5'-*TP*AP*AP*CP*CP*CP*TP*AP*A-3')

A: DNA (5'-*TP*AP*AP*CP*CP*CP*TP*AP*A-3')

A: DNA (5'-*TP*AP*AP*CP*CP*CP*TP*AP*A-3')

A: DNA (5'-*TP*AP*AP*CP*CP*CP*TP*AP*A-3')


Theoretical massNumber of molelcules
Total (without water)10,7354
Polymers10,7354
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation12_565x,x-y+1,-z+1/31
crystal symmetry operation9_555-x,-x+y,-z+1/31
Unit cell
Length a, b, c (Å)31.900, 31.900, 81.880
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: DNA chain DNA (5'-*TP*AP*AP*CP*CP*CP*TP*AP*A-3')


Mass: 2683.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 2.25 Å3/Da / Density % sol: 45.5 % / Description: hexagonal rods
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% PEG 400, 5 mM spermine, 50 mM 2-(N-morpholino)ethanesulfonic acid (MES)
PH range: 4.5-5.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
31001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0211
SYNCHROTRONDiamond I2323.0996
SYNCHROTRONDiamond I0230.92007
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELApr 25, 2013
DECTRIS PILATUS 12M2PIXELFeb 18, 2016
DECTRIS PILATUS 2M3PIXELFeb 7, 2016
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(III)SINGLE WAVELENGTHMx-ray1
2SI(III)SINGLE WAVELENGTHMx-ray2
3SI(III)SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
111
23.09961
30.920071
ReflectionResolution: 2.9→27.63 Å / Num. obs: 704 / % possible obs: 99.7 % / Redundancy: 30.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.007 / Rrim(I) all: 0.037 / Net I/σ(I): 79.6 / Num. measured all: 21199
Reflection shell

Rpim(I) all: 0.011 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.9-3.2533.70.04518310.04699
6.49-27.6320.70.036860.9990.03799.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0257refinement
XDSdata reduction
Aimless0.7.4data scaling
SHELXDEphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.95→25 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.909 / SU B: 16.599 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.358
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 30 4.4 %RANDOM
Rwork0.2389 ---
obs0.2384 647 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 121.8 Å2 / Biso mean: 49.393 Å2 / Biso min: 27.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0.14 Å2-0 Å2
2---0.27 Å20 Å2
3---0.88 Å2
Refinement stepCycle: final / Resolution: 2.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 178 0 0 178
Num. residues----9
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.011199
X-RAY DIFFRACTIONr_bond_other_d00.02102
X-RAY DIFFRACTIONr_angle_refined_deg0.941.187304
X-RAY DIFFRACTIONr_angle_other_deg1.6333241
X-RAY DIFFRACTIONr_chiral_restr0.0660.227
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02105
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0246
LS refinement shellResolution: 2.95→3.026 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 1 -
Rwork0.438 41 -
all-42 -
obs--97.67 %

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