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- PDB-1dnt: RNA/DNA DODECAMER R(GC)D(GTATACGC) WITH MAGNESIUM BINDING SITES -

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Basic information

Entry
Database: PDB / ID: 1dnt
TitleRNA/DNA DODECAMER R(GC)D(GTATACGC) WITH MAGNESIUM BINDING SITES
ComponentsDNA/RNA (5'-R(*GP*CP)-D(*GP*TP*AP*TP*AP*CP*GP*C)-3')
KeywordsDNA-RNA HYBRID / DNA CONFORMATION / RNA/DNA HYBRID / METAL IONS / DNA-RNA COMPLEX / DNA-RNA HYBRID COMPLEX
Function / homologyDNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRobinson, H. / Gao, Y.-G. / Sanishvili, R. / Joachimiak, A. / Wang, A.H.-J.
CitationJournal: Nucleic Acids Res. / Year: 2000
Title: Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes.
Authors: Robinson, H. / Gao, Y.G. / Sanishvili, R. / Joachimiak, A. / Wang, A.H.
History
DepositionDec 16, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2000Provider: 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 / Structure summary / Category: software / struct_keywords / Item: _struct_keywords.text
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/RNA (5'-R(*GP*CP)-D(*GP*TP*AP*TP*AP*CP*GP*C)-3')
B: DNA/RNA (5'-R(*GP*CP)-D(*GP*TP*AP*TP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1783
Polymers6,1542
Non-polymers241
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.538, 43.725, 45.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-R(*GP*CP)-D(*GP*TP*AP*TP*AP*CP*GP*C)-3')


Mass: 3077.005 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.: 51 / 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: 1.87 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPD, CACODYLATE, MGCL2, SPERMINE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1CACODYLATE11
2SPERMINE11
3MGCL211
4MPD11
5MPD12
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDDetailsSol-IDChemical formula
15 mMDNA duplex10.0025ml
2100 mMsodium cacodylate10.0010ml
320 %MPD10.005ml
415 mMspermine10.0025ml
5100 mM10.0025ml1MgCl2

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 17, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→10 Å / Num. all: 5962 / Num. obs: 5929 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 43.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 11.5 / % possible all: 100

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Processing

Software
NameClassification
d*TREKdata reduction
X-PLORmodel building
SHELXL-97refinement
d*TREKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→10 Å / Num. parameters: 1843 / Num. restraintsaints: 1769 / Cross valid method: A POSTERIORI / σ(F): 0 / σ(I): 0 / Stereochemistry target values: G.PARKINSON ET AL.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 295 5 %RANDOM
Rwork0.194 ---
all0.196 5929 --
obs0.194 5929 99.3 %-
Solvent computationSolvent model: SHELXL SWAT OPTION
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 460
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 408 7 45 460
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.061
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.005
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.059
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 5900 / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.061

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