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- PDB-1dou: MONOVALENT CATIONS SEQUESTER WITHIN THE A-TRACT MINOR GROOVE OF [... -

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Basic information

Entry
Database: PDB / ID: 1dou
TitleMONOVALENT CATIONS SEQUESTER WITHIN THE A-TRACT MINOR GROOVE OF [D(CGCGAATTCGCG)]2
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / DODECAMER / CATION BINDING
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.82 Å
AuthorsWoods, K.K. / McFail-Isom, L. / Sines, C.C. / Howerton, S.B. / Stephens, R.K. / Williams, L.D.
CitationJournal: J.Am.Chem.Soc. / Year: 2000
Title: Monovalent Cations Sequester within the A-Tract Minor Groove of [d(CGCGAATTCGCG)]2
Authors: Woods, K.K. / McFail-Isom, L. / Sines, C.C. / Howerton, S.B. / Stephens, R.K. / Williams, L.D.
History
DepositionDec 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3513
Polymers7,3272
Non-polymers241
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.296, 40.243, 65.939
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.52
Details: SSDNA, CESIUM CACODYLATE, MPD, SPERMINE, MGCL2, pH 6.52, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1CESIUM CACODYLATE11
2SPERMINE11
3MGCL211
4MPD11
5MPD12
Crystal grow
*PLUS
pH: 6.9 / Details: Tereshko, V., (1999) J. Am. Chem. Soc., 121, 470.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.2 mMDNA1drop
220 mMsodium cacodylate1drop
325 mM1dropMg(OAc)2
43 mMspermine 4HCl1drop
540 %1reservoir

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Data collection

DiffractionMean temperature: 163 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER / Wavelength: 0.7107
DetectorType: BRUKER / Detector: CCD / Date: Jan 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7107 Å / Relative weight: 1
ReflectionResolution: 1.82→10 Å / Num. all: 11550 / Num. obs: 8665 / Observed criterion σ(F): 3 / Redundancy: 10 %
Reflection shellResolution: 1.82→1.93 Å / % possible all: 52

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
SMART(BRUKER)data reduction
X-PLORphasing
RefinementResolution: 1.82→10 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.267 866 10 %RANDOM
Rwork0.209 ---
obs0.209 8665 --
all-11550 --
Refinement stepCycle: LAST / Resolution: 1.82→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 7 141 634
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.038
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 3 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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