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- PDB-208d: HIGH-RESOLUTION STRUCTURE OF A DNA HELIX FORMING (C.G)*G BASE TRIPLETS -

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Basic information

Entry
Database: PDB / ID: 208d
TitleHIGH-RESOLUTION STRUCTURE OF A DNA HELIX FORMING (C.G)*G BASE TRIPLETS
ComponentsDNA (5'-D(*GP*CP*GP*AP*AP*TP*TP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / BASE TRIPLET
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsVan Meervelt, L. / Vlieghe, D. / Dautant, A. / Gallois, B. / Precigoux, G. / Kennard, O.
Citation
Journal: Nature / Year: 1995
Title: High-resolution structure of a DNA helix forming (C.G)*G base triplets.
Authors: Van Meervelt, L. / Vlieghe, D. / Dautant, A. / Gallois, B. / Precigoux, G. / Kennard, O.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Formation of (C.G)*G Triplets in a B-DNA Duplex with Overhanging Bases
Authors: Vlieghe, D. / Van Meervelt, L. / Dautant, A. / Gallois, B. / Precigoux, G. / Kennard, O.
History
DepositionApr 26, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,5604
Polymers5,5122
Non-polymers492
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)22.238, 37.010, 54.100
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 DNA (5'-D(*GP*CP*GP*AP*AP*TP*TP*CP*G)-3')


Mass: 2755.823 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, temperature 289.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE11
5WATER12
6MPD12
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mMDNA1drop
254 mM1dropMgCl2
32.4 mMspermine1drop
411 %MPD1drop
550 %MPD1reservoir
61

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 2, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. all: 22402 / Num. obs: 2824 / % possible obs: 87 % / Observed criterion σ(I): 3 / Redundancy: 7.9 % / Rmerge(I) obs: 0.036
Reflection
*PLUS
Highest resolution: 2.05 Å / % possible obs: 87 % / Observed criterion σ(I): 3

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Processing

Software
NameClassification
AMoREphasing
X-PLORrefinement
IPMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BDL001

Resolution: 2.05→8 Å / σ(F): 4
RfactorNum. reflection% reflection
Rwork0.168 --
obs0.168 2379 79.5 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.05→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 366 2 86 454
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3.21
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.88
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 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 8 Å / σ(F): 4
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.883

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