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- PDB-1jgr: Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATTCGCG wi... -

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Basic information

Entry
Database: PDB / ID: 1jgr
TitleCrystal Structure Analysis of the B-DNA Dodecamer CGCGAATTCGCG with Thallium Ions.
Components5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
KeywordsDNA / DOUBLE HELIX / DEOXYRIBONUCLEIC ACID / THALLIUM
Function / homologyTHALLIUM (I) ION / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsHowerton, S.B. / Sines, C.C. / VanDerveer, D. / Williams, L.D.
CitationJournal: Biochemistry / Year: 2001
Title: Locating monovalent cations in the grooves of B-DNA.
Authors: Howerton, S.B. / Sines, C.C. / VanDerveer, D. / Williams, L.D.
History
DepositionJun 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,00816
Polymers7,3272
Non-polymers2,68114
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.944, 40.744, 66.202
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*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: Chemical
ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Tl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: DNA, thallium acetate, magnesium acetate, MPD, spermine acetate, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1DNA11
2thallium acetate11
3magnesium acetate11
4MPD11
5spermine acetate11
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.0 mMammonium salt1drop
219 mMthallium(I) acetate1drop
35.2 mM1drop
43.8 %1drop
58.9 mM1drop
635 %MPD1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS X26C11.1
ROTATING ANODERIGAKU RU30021.5418
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDMay 26, 2000graphite monochromator
RIGAKU RAXIS IV++2IMAGE PLATEMay 4, 2001OSMIC BLUE CONFOCAL
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.54181
ReflectionResolution: 1.14→35 Å / Num. all: 21760 / Num. obs: 21760 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 16.72 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.4
Reflection shellResolution: 1.2→1.28 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.144 / Num. unique all: 3249 / % possible all: 68
Reflection
*PLUS
Lowest resolution: 35 Å / % possible obs: 93 % / Num. measured all: 290894
Reflection shell
*PLUS
% possible obs: 68 %

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Processing

Software
NameVersionClassification
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementStarting model: PDB ENTRY 1FQN

1fqn


Resolution: 1.2→10 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: R FREE / σ(F): 2 / σ(I): 2 / Stereochemistry target values: PARKINSON et al.
RfactorNum. reflectionSelection details
Rfree0.222 2100 RANDOM
Rwork0.169 --
all0.173 20997 -
obs0.163 17667 -
Displacement parametersBiso mean: 19.5 Å2
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 20 134 640
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.004
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 35 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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