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- PDB-1zf3: ATC Four-stranded DNA Holliday Junction -

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Basic information

Entry
Database: PDB / ID: 1zf3
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: 1.84 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
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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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)6,1303
Polymers6,0902
Non-polymers401
Water2,702150
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)12,2606
Polymers12,1804
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Unit cell
Length a, b, c (Å)64.95, 24.62, 37.46
Angle α, β, γ (deg.)90.00, 112.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-160-

HOH

21B-45-

HOH

31B-135-

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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
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-BM-D / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.84→99 Å / Num. obs: 4856 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Χ2: 1.034 / Net I/σ(I): 15
Reflection shellResolution: 1.84→1.92 Å / % possible obs: 96.9 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 1.07 / Num. measured obs: 465 / Rsym value: 0.626 / Χ2: 1.024 / % possible all: 96.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
HKL-2000data reduction
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ndb entry UD0058

Resolution: 1.84→30.08 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.851 / SU B: 6.34 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.231 472 10.4 %RANDOM
Rwork0.202 ---
all0.205 ---
obs0.248 4063 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: 9.615 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.1 Å2
2--0.33 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.84→30.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 1 150 555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021452
X-RAY DIFFRACTIONr_angle_refined_deg1.6633694
X-RAY DIFFRACTIONr_chiral_restr0.0740.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02206
X-RAY DIFFRACTIONr_nbd_refined0.2780.2226
X-RAY DIFFRACTIONr_nbtor_refined0.310.2262
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2710.2132
X-RAY DIFFRACTIONPOTENTIAL METAL-ION REFINED ATOMS (A)0.2230.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.231
X-RAY DIFFRACTIONr_scbond_it1.2513648
X-RAY DIFFRACTIONr_scangle_it1.5894.5694
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 19 -
Rwork0.294 176 -
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)
10.5920.24520.10330.10150.04280.018-0.02390.0022-0.01220.0378-0.05740.00410.0730.05790.08130.00560.0179-0.0051-0.00670.0136-0.004425.76030.441232.701
21.9964-0.4140.22870.2581-0.39830.7411-0.0319-0.00170.070.02710.0181-0.10040.0804-0.0790.01380.0213-0.0036-0.0041-0.017-0.0247-0.005121.13020.509126.1638
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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