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- PDB-2af1: Structure of the DNA coiled-coil formed by d(CGATATATATAT) -

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Basic information

Entry
Database: PDB / ID: 2af1
TitleStructure of the DNA coiled-coil formed by d(CGATATATATAT)
Components5'-D(*CP*GP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3'
KeywordsDNA / HOOGSTEEN H-BONDS / COILED-COIL
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsDe Luchi, D. / Tereshko, V. / Gouyette, C. / Subirana, J.A.
CitationJournal: Chembiochem / Year: 2006
Title: Structure of the DNA Coiled Coil Formed by d(CGATATATATAT)
Authors: De Luchi, D. / Tereshko, V. / Gouyette, C. / Subirana, J.A.
History
DepositionJul 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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
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: 5'-D(*CP*GP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3'


Theoretical massNumber of molelcules
Total (without water)3,6601
Polymers3,6601
Non-polymers00
Water00
1
A: 5'-D(*CP*GP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3'

A: 5'-D(*CP*GP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3'


Theoretical massNumber of molelcules
Total (without water)7,3212
Polymers7,3212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)26.541, 26.541, 220.527
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: DNA chain 5'-D(*CP*GP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3'


Mass: 3660.428 Da / Num. of mol.: 1 / Source method: obtained synthetically

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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: 3.3 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: cacodylate,MPD, sodium phosphate, potassium chloride, Trimethylamine-N-oxide, spermine , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylate11
2MPD11
3sodium phosphate11
4potassium chloride11
5Trimethylamine-N-oxide11
6spermine11
7H2O11
8cacodylate12
9MPD12
10sodium phosphate12
11potassium chloride12
12H2O12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.972 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 3.1→23 Å / Num. all: 1101 / Num. obs: 1099 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 3.1 Å / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1GQU

1gqu


Resolution: 3.1→23 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.946 / SU B: 45.734 / SU ML: 0.75 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 5.02 / ESU R Free: 0.554 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.34585 115 10.5 %RANDOM
Rwork0.3316 ---
obs0.33318 983 99.82 %-
all-985 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å20 Å2
2---0.32 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 3.1→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 243 0 0 243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021272
X-RAY DIFFRACTIONr_angle_refined_deg1.983418
X-RAY DIFFRACTIONr_chiral_restr0.0870.247
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02126
X-RAY DIFFRACTIONr_nbd_refined0.2480.2119
X-RAY DIFFRACTIONr_nbtor_refined0.3140.2152
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2980.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.29
X-RAY DIFFRACTIONr_scbond_it03389
X-RAY DIFFRACTIONr_scangle_it04.5418
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.612 9 -
Rwork0.541 62 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 17.858 Å / Origin y: 6.857 Å / Origin z: 89.525 Å
111213212223313233
T0.3179 Å2-0.0465 Å2-0.0543 Å2-0.4424 Å20.0078 Å2--0.2198 Å2
L3.1157 °21.2362 °2-6.2853 °2-8.7648 °2-9.2344 °2--18.1706 °2
S-0.0855 Å °-0.0718 Å °0.5401 Å °-0.733 Å °-0.6916 Å °-0.1924 Å °-0.5044 Å °1.3114 Å °0.777 Å °

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