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- PDB-1zfh: TTA Duplex B-DNA -

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Basic information

Entry
Database: PDB / ID: 1zfh
TitleTTA Duplex B-DNA
Components5'-D(*CP*CP*TP*AP*AP*TP*TP*AP*GP*G)-3'
KeywordsDNA / Crystallographic Screen / DNA Structure / Holliday Junction / Molecular Structure
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsHays, F.A. / Teegarden, A.T. / Jones, Z.J.R. / Harms, M. / Raup, D. / Watson, J. / Cavaliere, E. / Ho, P.S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: How sequence defines structure: a crystallographic map of DNA structure and conformation.
Authors: Hays, F.A. / Teegarden, A. / Jones, Z.J. / Harms, M. / Raup, D. / Watson, J. / Cavaliere, E. / Ho, P.S.
History
DepositionApr 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,0882
Polymers6,0882
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.807, 24.348, 41.852
Angle α, β, γ (deg.)90.00, 122.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 3044.016 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5'-TERMINAL NUCLEOTIDE THEN DEPROTECTED BY ...Details: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5'-TERMINAL NUCLEOTIDE THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN.
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 298 K / pH: 7
Details: Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00
Components of the solutions
IDNameCrystal-IDSol-ID
1Na Cacodylate11
2CaCl211
3Spermine11
4MPD11
5H2O11
6Na Cacodylate12
7CaCl212
8MPD12
9H2O12

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→99 Å / Num. obs: 1742 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.038 / Net I/σ(I): 16.5
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 1.3 / % possible all: 67.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0003refinement
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ENTRY BD0028

Resolution: 2.51→17.6 Å / Cor.coef. Fo:Fc: 0.733 / Cor.coef. Fo:Fc free: 0.697 / SU B: 14.397 / SU ML: 0.341 / Cross valid method: THROUGHOUT / ESU R Free: 0.503 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: STRUCTURE IS NOT REFINED TO ITS LOWEST R AND RFREE VALUES. PLEASE REFER TO CITATION ABOVE FOR DETAILS. COORDINATES WILL BE UPDATED AS A MORE REFINED MODEL IS OBTAINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.359 155 9.6 %RANDOM
Rwork0.32 ---
obs0.324 1458 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 4.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20.29 Å2
2--0.05 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.51→17.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 21 425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9433694
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1350.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02204
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3670.2228
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3440.2252
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3560.221
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.470.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.470.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it0.8813636
X-RAY DIFFRACTIONr_scangle_it1.4124.5694
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.775 4 -
Rwork0.365 48 -
obs--100 %

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