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- PDB-1zf4: ATC Four-stranded DNA Holliday Junction -

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Basic information

Entry
Database: PDB / ID: 1zf4
TitleATC Four-stranded DNA Holliday Junction
Components5'-D(*CP*CP*GP*AP*TP*AP*TP*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: 1.65 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: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 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: 5'-D(*CP*CP*GP*AP*TP*AP*TP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*AP*TP*AP*TP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1133
Polymers6,0902
Non-polymers231
Water2,126118
1
A: 5'-D(*CP*CP*GP*AP*TP*AP*TP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*AP*TP*AP*TP*CP*GP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)12,2266
Polymers12,1804
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Unit cell
Length a, b, c (Å)64.936, 24.034, 40.286
Angle α, β, γ (deg.)90.00, 118.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-68-

NA

21A-127-

HOH

31B-88-

HOH

41B-116-

HOH

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Components

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


Mass: 3045.005 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Na 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

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.072 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.65→12.7 Å / Num. obs: 5414 / % possible obs: 79.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.055 / Rsym value: 0.054 / Χ2: 1.051 / Net I/σ(I): 15.5
Reflection shellResolution: 1.65→1.71 Å / % possible obs: 32.7 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 3.8 / Num. measured obs: 216 / Rsym value: 0.179 / Χ2: 0.68 / % possible all: 48.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ndb entry UD0058

Resolution: 1.65→12.7 Å / Cor.coef. Fo:Fc: 0.856 / Cor.coef. Fo:Fc free: 0.788 / SU B: 5.511 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.275 555 10.2 %RANDOM
Rwork0.231 ---
obs0.268 4894 96.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.578 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20.04 Å2
2--0.82 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.65→12.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 1 118 523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021452
X-RAY DIFFRACTIONr_angle_refined_deg1.7943694
X-RAY DIFFRACTIONr_chiral_restr0.070.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02206
X-RAY DIFFRACTIONr_nbd_refined0.2760.2197
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2265
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2890.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3170.221
X-RAY DIFFRACTIONr_scbond_it1.3173535
X-RAY DIFFRACTIONr_scangle_it1.6684.5694
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 24 -
Rwork0.275 245 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.42080.5614-1.03390.2688-0.78423.75660.00450.0294-0.13180.0216-0.1068-0.0584-0.0602-0.04890.1023-0.00770.00480.0057-0.0503-0.0137-0.017857.4101-0.59051.7341
21.87360.51760.09080.39220.70011.8325-0.0908-0.13120.0029-0.05340.0940.0126-0.0376-0.0321-0.0032-0.0195-0.0203-0.0073-0.01530.0276-0.020961.9825-0.3018.6491
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Label seq-ID: 1 - 10

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-ID
11AA1 - 10
22BB11 - 20

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