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- PDB-1zfa: GGA Duplex A-DNA -

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Basic information

Entry
Database: PDB / ID: 1zfa
TitleGGA Duplex A-DNA
Components5'-D(*CP*CP*TP*CP*CP*GP*GP*AP*GP*G)-3'
KeywordsDNA / Crystallographic Screen / DNA Structure / Holliday Junction / Molecular Structure
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.56 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 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,2016
Polymers6,0922
Non-polymers1094
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.930, 44.620, 46.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3045.992 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.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / 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: 2.05 Å3/Da / Density % sol: 39.99 %
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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.5→99 Å / Num. obs: 8318 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 4.1 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 12.5
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.233

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ZF9

1zf9


Resolution: 1.56→19.23 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 45057.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: STRUCTURE HAS NOT BEEN REFINED TO ITS LOWEST R AND RFREE VALUES. REFER TO CITATION ABOVE FOR
RfactorNum. reflection% reflectionSelection details
Rfree0.3 788 10.6 %RANDOM
Rwork0.241 ---
obs0.241 7429 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.6038 Å2 / ksol: 0.273898 e/Å3
Displacement parametersBiso mean: 6.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.309 Å20 Å20 Å2
2--0.378 Å20 Å2
3----0.069 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.56→19.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 4 130 538
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.024
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_deg3.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d29.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.19
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.213
X-RAY DIFFRACTIONc_mcangle_it1.3170
X-RAY DIFFRACTIONc_scbond_it1.9780
X-RAY DIFFRACTIONc_scangle_it2.5070
LS refinement shellResolution: 1.56→1.66 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 114 9.7 %
Rwork0.245 1060 -
obs--96.5 %
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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