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- PDB-1i5w: A-DNA DECAMER GCGTA(TLN)ACGC -

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Basic information

Entry
Database: PDB / ID: 1i5w
TitleA-DNA DECAMER GCGTA(TLN)ACGC
Components5'-D(*GP*CP*GP*TP*AP*(TLN)P*AP*CP*GP*C)-3'
KeywordsDNA / A-DNA decamer / locked ribonucleotide.
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsEgli, M. / Minasov, G. / Teplova, M. / Kumar, R. / Wengel, J.
CitationJournal: J.Chem.Soc.,Chem.Commun. / Year: 2001
Title: X-ray crystal structure of a locked nucleic acid (LNA) duplex composed of a palindromic 10-mer DNA strand containing one LNA thymine monomer
Authors: Egli, M. / Minasov, G. / Teplova, M. / Kumar, R. / Wengel, J.
History
DepositionMar 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*CP*GP*TP*AP*(TLN)P*AP*CP*GP*C)-3'
B: 5'-D(*GP*CP*GP*TP*AP*(TLN)P*AP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,1462
Polymers6,1462
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.140, 43.960, 45.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsThe biological assembly is a duplex generated by the two fold axis.

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Components

#1: DNA chain 5'-D(*GP*CP*GP*TP*AP*(TLN)P*AP*CP*GP*C)-3'


Mass: 3073.016 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.06 Å3/Da / Density % sol: 40.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MPD, Spermine, KCl, Sodium Cacodylate, pH 6.0. VAPOR DIFFUSION, HANGING DROP at 295 K, temperature 295.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2Sodium Cacodylate11
3Spermine11
4MPD11
5MPD12
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.8 mMdecamer solution1drop
210 %MPD1drop
340 mMsodium cacodylate1drop
412 mMspermine tetrahydrochloride1drop
580 mMpotassium chloride1drop
635 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.93217 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 31, 1999
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93217 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. all: 10950 / Num. obs: 10950 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 38.5
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 6.8 / Num. unique all: 1038 / % possible all: 96.7
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A-DNA decamer

Resolution: 1.4→17 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Parkinson et al. / Details: Maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.174 1036 9.7 %Random
Rwork0.167 ---
all-10660 --
obs-10660 97.5 %-
Displacement parametersBiso mean: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.542 Å20 Å20 Å2
2--2.174 Å20 Å2
3----0.632 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.4→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 416 0 128 544
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.51
X-RAY DIFFRACTIONc_dihedral_angle_d27.46
X-RAY DIFFRACTIONc_improper_angle_d1.62
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDTotal num. of bins used% reflection obs (%)
1.4-1.450.2828790.2589X-RAY DIFFRACTION100.941
1.45-1.510.23691060.2201X-RAY DIFFRACTION100.954
1.51-1.580.22711050.2036X-RAY DIFFRACTION100.965
1.58-1.660.19231060.1653X-RAY DIFFRACTION100.975
1.66-1.760.21111070.1627X-RAY DIFFRACTION100.984
1.76-1.90.1683900.1595X-RAY DIFFRACTION100.983
1.9-2.090.20621110.1728X-RAY DIFFRACTION100.991
2.09-2.390.18071080.1709X-RAY DIFFRACTION100.995
2.39-3.010.18271260.173X-RAY DIFFRACTION100.998
3.01-170.1307980.1497X-RAY DIFFRACTION100.998
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.46
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.62

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