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- PDB-1zf1: CCC A-DNA -

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Basic information

Entry
Database: PDB / ID: 1zf1
TitleCCC A-DNA
Components5'-D(*CP*CP*GP*GP*GP*CP*CP*CP*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: 1.35 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 19, 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
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*GP*GP*GP*CP*CP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*GP*GP*CP*CP*CP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,0942
Polymers6,0942
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.80, 44.37, 46.25
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3046.980 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.: 130 / 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: 2.09 Å3/Da / Density % sol: 41.09 %
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 25, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.18→99 Å / Num. obs: 16256 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 6.4 Å2 / Rmerge(I) obs: 0.028
Reflection shellResolution: 1.18→1.22 Å / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 1.37 / Rsym value: 0.453 / % possible all: 49.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
HKL-2000data reduction
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ENTRY ADJ082

Resolution: 1.35→19.61 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 49500.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: STRUCTURE IS NOT REFINED TO ITS LOWEST R VALUES, REFER TO CITATION. ALTERNATE CONFORMATIONS CLEARLY VISIBLE ALONG DNA BACKBONE.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1151 10.2 %RANDOM
Rwork0.222 ---
obs0.222 11315 96.5 %-
Solvent computationBsol: 24.42 Å2
Displacement parametersBiso mean: 8.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.424 Å20 Å20 Å2
2--0.576 Å20 Å2
3----0.152 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.35→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 130 534
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d33.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.752
X-RAY DIFFRACTIONc_mcangle_it0.9730
X-RAY DIFFRACTIONc_scbond_it1.1340
X-RAY DIFFRACTIONc_scangle_it1.7120
LS refinement shellResolution: 1.35→1.43 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 188 10.5 %
Rwork0.258 1597 -
obs--93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:DNA-RNA_REP.PARAMCNS_TOPPAR:DNA-RNA.TOP
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARAMCNS_TOPPAR:DNA-RNA.LINK
X-RAY DIFFRACTION3CNS_TOPPAR:ION.PARAMCNS_TOPPAR:WATER.TOP
X-RAY DIFFRACTION4CNS_TOPPAR:ION.TOP

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