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- PDB-1zf2: Four-stranded DNA Holliday Junction (CCC) -

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Basic information

Entry
Database: PDB / ID: 1zf2
TitleFour-stranded DNA Holliday Junction (CCC)
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: 1.95 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
Water1,15364
1
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'

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)12,1884
Polymers12,1884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)64.960, 24.710, 36.760
Angle α, β, γ (deg.)90.00, 110.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-29-

HOH

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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.: 64 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2645.68
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, sitting drop7Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
2982vapor diffusion, sitting drop7Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Na Cacodylate11
2CaCl211
3Spermine11
4MPD11
5H2O11
6Na Cacodylate12
7CaCl212
8MPD12
9H2O12
10Na Cacodylate21
12CaCl221
13Spermine21
14MPD21
15H2O21
16Na Cacodylate22
17CaCl222
18MPD22
19H2O22

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21031
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-ID-B10.827
SYNCHROTRONAPS 14-ID-B20.827
Detector
TypeIDDetectorDate
MARRESEARCH1CCDFeb 26, 2004
MARRESEARCH2CCDFeb 26, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.88→16 Å / Num. obs: 3883 / % possible obs: 88.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 4.3 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 8
Reflection shellResolution: 1.88→2.02 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.335 / % possible all: 65.9

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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 UD0028

Resolution: 1.95→16 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 57150.59 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: STRUCTURE IS NOT CURRENTLY REFINED TO ITS LOWEST R VALUES, PLEASE REFER TO CITATION FOR MORE
RfactorNum. reflection% reflectionSelection details
Rfree0.273 349 10 %RANDOM
Rwork0.231 ---
obs0.231 3477 84.3 %-
Solvent computationBsol: 45.44 Å2
Displacement parametersBiso mean: 11.76 Å2
Baniso -1Baniso -2Baniso -3
1--1.016 Å20 Å20.593 Å2
2---0.946 Å20 Å2
3---1.962 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.95→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 64 468
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.562
X-RAY DIFFRACTIONc_mcangle_it0.7580
X-RAY DIFFRACTIONc_scbond_it1.10
X-RAY DIFFRACTIONc_scangle_it1.5680
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 69 12.7 %
Rwork0.24 474 -
obs--79 %
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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