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- PDB-417d: A THYMINE-LIKE BASE ANALOGUE FORMS WOBBLE PAIRS WITH ADENINE -

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Basic information

Entry
Database: PDB / ID: 417d
TitleA THYMINE-LIKE BASE ANALOGUE FORMS WOBBLE PAIRS WITH ADENINE
ComponentsDNA (5'-D(*CP*AP*CP*GP*(C46)P*G)-3')
KeywordsDNA / P.A BASE-PAIRS / PYRIMIDINE ANALOGUE / Z-DNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLin, P.K.T. / Schuerman, M.H. / Moore, G.S. / Van Meervelt, L. / Loakes, D. / Brown, D.M. / Moore, M.H.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: A thymine-like base analogue forms wobble pairs with adenine in a Z-DNA duplex.
Authors: Schuerman, G.S. / Van Meervelt, L. / Loakes, D. / Brown, D.M. / Kong Thoo Lin, P. / Moore, M.H. / Salisbury, S.A.
History
DepositionJul 15, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 30, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _software.name / _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: DNA (5'-D(*CP*AP*CP*GP*(C46)P*G)-3')
B: DNA (5'-D(*CP*AP*CP*GP*(C46)P*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6722
Polymers3,6722
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.338, 31.432, 44.486
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*CP*AP*CP*GP*(C46)P*G)-3')


Mass: 1836.243 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1.65 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: CRYSTALS WERE OBTAINED FROM A SOLUTION THAT CONTAINED NA CACODYLATE, MG CHLORIDE, SPERMINE, MPD., pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1NA CACODYLATE11
2MGCL211
3SPERMINE11
4MPD11
5MPD12
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14.8 mMoligonucleotide1dropsingle stranded
22.5 mMsodium cacodylate1drop
320 mM1dropMgCl2
45 mMspermine1drop
51.6 %(v/v)1drop
6100 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 19, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.53→10 Å / Num. all: 3920 / Num. obs: 3920 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 21.08
Reflection shellResolution: 1.53→1.56 Å / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 11.92 / % possible all: 92.5

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Processing

Software
NameVersionClassification
AMoREphasing
SHELXL-93refinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB

Resolution: 1.5→10 Å / Num. parameters: 2724 / Num. restraintsaints: 5294 / σ(F): 4 / Stereochemistry target values: SHELXL
RfactorNum. reflection% reflectionSelection details
Rfree0.25 -10 %CCP4
Rwork0.155 ---
all0.156 3920 --
obs0.15 3696 97.5 %-
Solvent computationSolvent model: BABINET'S PRINCIPLE
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 244 0 58 302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.014
X-RAY DIFFRACTIONs_similar_dist0.02
X-RAY DIFFRACTIONs_from_restr_planes0.041
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.02
X-RAY DIFFRACTIONs_approx_iso_adps0.058
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 10 Å / σ(F): 4
Solvent computation
*PLUS
Displacement parameters
*PLUS

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