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- PDB-1omk: The Crystal Structure of d(CACG(5IU)G) -

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Basic information

Entry
Database: PDB / ID: 1omk
TitleThe Crystal Structure of d(CACG(5IU)G)
Components5'-D(*CP*AP*CP*GP*(5IU)P*G)-3'
KeywordsDNA / Z-DNA / 5-IODO-2'-DEOXYURIDINE
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSchuerman, G. / Van Hecke, K. / Van Meervelt, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Exploration of the influence of 5-iodo-2'-deoxyuridine incorporation on the structure of d[CACG(IDU)G].
Authors: Schuerman, G. / Van Hecke, K. / Van Meervelt, L.
History
DepositionFeb 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
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 / diffrn_source / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,1644
Polymers3,8422
Non-polymers3222
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)18.155, 30.034, 41.988
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*AP*CP*GP*(5IU)P*G)-3'


Mass: 1921.087 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THE OLIGONUCLEOTIDE WAS SYNTHESIZED BY THE REGA-INSTITUTE KULEUVEN
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 1.49 Å3/Da / Density % sol: 17.43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: potassium cacodylate, MPD, magnesium chloride, potassium chloride, cobalt hexamine , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1potassium cacodylate11
2MPD11
3magnesium chloride11
4potassium chloride11
5cobalt hexamine11
6MPD12
7potassium cacodylate12
8magnesium chloride12
9potassium chloride12
Crystal grow
*PLUS
pH: 6.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.66 mg/mlprotein1drop
228.7 mMpotassium cacodylate1droppH6.9
324.5 %(v/v)MPD1drop
440 mMpotassium cacodylate1reservoirpH5.5
56 mMcobalt hexammine1reservoir
680 mM1reservoirKCl
720 mM1reservoirMgCl2
810 %(v/v)MPD1reservoir
91

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. all: 6103 / Num. obs: 5988 / % possible obs: 98.2 % / Redundancy: 22.9 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.062
Reflection shellResolution: 1.3→1.35 Å / Rmerge(I) obs: 0.165 / Num. unique all: 903 / % possible all: 98.8
Reflection
*PLUS
Num. measured all: 137352
Reflection shell
*PLUS
% possible obs: 98.8 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXLrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ENTRY ZDFB51

Resolution: 1.3→20 Å / Isotropic thermal model: Isotropic / σ(F): 4 / Details: The iodo atoms are refined anisotropically /
Num. reflection% reflection
all5988 -
obs5036 98.2 %
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 14 43 297
Software
*PLUS
Name: SHELXL / Version: 93 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS

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