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- PDB-6adv: Crystal Structure Analysis of the duplex containing the S2T(2',4'... -

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Basic information

Entry
Database: PDB / ID: 6adv
TitleCrystal Structure Analysis of the duplex containing the S2T(2',4'-BNA/LNA)G mismatch pairs
Components5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(9V9)P*GP*CP*G)-3'
KeywordsDNA / LNA / 2' / 4'-BNA / mismatched base pairs
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsAoyama, H.A. / Habuchi, T.H. / Yamaguchi, T.Y. / Obika, S.O.
CitationJournal: J. Org. Chem. / Year: 2019
Title: Hybridization and Mismatch Discrimination Abilities of 2',4'-Bridged Nucleic Acids Bearing 2-Thiothymine or 2-Selenothymine Nucleobase.
Authors: Habuchi, T. / Yamaguchi, T. / Aoyama, H. / Horiba, M. / Ito, K.R. / Obika, S.
History
DepositionAug 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(9V9)P*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(9V9)P*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,4452
Polymers7,4452
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.490, 41.130, 65.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DC / Beg label comp-ID: DC / End auth comp-ID: DG / End label comp-ID: DG / Refine code: 4 / Auth seq-ID: 1 - 12 / Label seq-ID: 1 - 12

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.782722, 0.619355, -0.061197), (0.618399, -0.785049, -0.035786), (-0.070207, -0.009834, -0.997484)-1.66759, 2.27009, -18.022881

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Components

#1: DNA chain 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(9V9)P*GP*CP*G)-3'


Mass: 3722.479 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.21 Å3/Da / Density % sol: 44.47 % / Mosaicity: 0.9 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 7 / Details: 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.96→32.71 Å / Num. obs: 5231 / % possible obs: 98.7 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 12.1 / Num. measured all: 34495 / Scaling rejects: 146
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.96-2.016.60.8083510.8260.3310.87599.7
8.98-32.714.90.055370.9970.0260.06148.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.96 Å17.41 Å
Translation1.96 Å17.41 Å

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Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
PHASER2.5.6phasing
REFMAC5.8.0069refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1d27

1d27


Resolution: 1.96→32.71 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 15.831 / SU ML: 0.2 / SU R Cruickshank DPI: 0.2261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.2
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2968 491 9.5 %RANDOM
Rwork0.2531 ---
obs0.2576 4680 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 88.42 Å2 / Biso mean: 50.518 Å2 / Biso min: 31.48 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å2-0 Å20 Å2
2--4.01 Å2-0 Å2
3----1.98 Å2
Refinement stepCycle: final / Resolution: 1.96→32.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 492 0 15 507
Biso mean---50.82 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.012552
X-RAY DIFFRACTIONr_bond_other_d0.0030.02272
X-RAY DIFFRACTIONr_angle_refined_deg2.5151.319854
X-RAY DIFFRACTIONr_angle_other_deg1.9113644
X-RAY DIFFRACTIONr_chiral_restr0.1370.274
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.019286
X-RAY DIFFRACTIONr_gen_planes_other0.0020.019116
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 382 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.80.5
MEDIUM THERMAL4.262
LS refinement shellResolution: 1.959→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 36 -
Rwork0.335 332 -
all-368 -
obs--97.61 %
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)
10.484-0.2271.43510.2633-1.31896.98570.17180.06650.01930.07020.00830.0556-0.16330.1458-0.18010.22320.01530.02980.07640.02160.0902-2.55751.1748-8.8141
20.46390.27191.30781.097-1.05857.73250.07650.08280.05460.14140.08650.1328-0.1630.1768-0.1630.10480.03430.04580.0644-0.01010.0663-2.02350.2284-9.0886
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 12
2X-RAY DIFFRACTION2B1 - 12

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