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- PDB-1d3r: CRYSTAL STRUCTURE OF TRIPLEX DNA -

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Basic information

Entry
Database: PDB / ID: 1d3r
TitleCRYSTAL STRUCTURE OF TRIPLEX DNA
Components
  • DNA (5'-D(*CP*(BRU)P*CP*CP*(BRU)P*CP*CP*GP*CP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*GP*CP*GP*GP*AP*G)-3')
KeywordsDNA / TRIPLEX DNA AND ITS JUNCTION WITH A DUPLEX DNA
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsRhee, S. / Han, Z.-J. / Liu, K. / Todd Miles, H.T. / Davies, D.R.
Citation
Journal: Biochemistry / Year: 1999
Title: Structure of a triple helical DNA with a triplex-duplex junction.
Authors: Rhee, S. / Han, Z. / Liu, K. / Miles, H.T. / Davies, D.R.
#1: Journal: To be Published / Year: 1999
Title: Crystallization and preliminary X-ray data of a triplex DNA
Authors: Rhee, S. / Davies, D.R.
History
DepositionSep 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 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 / 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*(BRU)P*CP*CP*(BRU)P*CP*CP*GP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*CP*GP*GP*AP*G)-3')
C: DNA (5'-D(*CP*(BRU)P*CP*CP*(BRU)P*CP*CP*GP*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*CP*GP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)12,9744
Polymers12,9744
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.800, 53.800, 43.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Cell settingtetragonal
Space group name H-MP42

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Components

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


Mass: 3705.058 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*CP*GP*CP*GP*GP*AP*G)-3')


Mass: 2781.823 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: MPD, NACL, MGCL2, SPERMINE, PH 5.2 AT 298 K, pH 5.20, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1NACL11
2MGCL211
3SPERMINE11
4MPD11
5MPD12
Crystal grow
*PLUS
pH: 5.04 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.04 Msodium cacodylate1drop
20.2 M1dropNaCl
30.1 M1dropMgCl2
40.01 Mspermine 4HCl1drop
512 %1drop
647 %MPD1reservoir
70.17 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9200, 0.919392, 0.914982
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 23, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
20.9193921
30.9149821
ReflectionResolution: 1.8→40 Å / Num. obs: 127674 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 13.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.404 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 40 Å / Observed criterion σ(I): -3

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Processing

Software
NameClassification
SHELXmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementResolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: PARKINSON ET AL.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 2375 10 %RANDOM
Rwork0.21 ---
obs0.21 21581 96.3 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 823 0 157 980
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Num. reflection all: 22407 / Rfactor all: 0.224 / Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg2.16

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