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- PDB-284d: THE BI-LOOP, A NEW GENERAL FOUR-STRANDED DNA MOTIF -

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Basic information

Entry
Database: PDB / ID: 284d
TitleTHE BI-LOOP, A NEW GENERAL FOUR-STRANDED DNA MOTIF
ComponentsDNA (5'-CD(*P*AP*TP*TP*CP*AP*TP*TP*C)-3')
KeywordsDNA / CYCLIC B-DNA / QUADRUPLE HELIX / BI-LOOP
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / HEAVY ATOM METHOD / Resolution: 1.1 Å
AuthorsSalisbury, S.A. / Wilson, S.E. / Powell, H.R. / Kennard, O. / Lubini, P. / Sheldrick, G.M. / Escaja, N. / Alazzouzi, E. / Grandas, A. / Pedroso, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: The bi-loop, a new general four-stranded DNA motif.
Authors: Salisbury, S.A. / Wilson, S.E. / Powell, H.R. / Kennard, O. / Lubini, P. / Sheldrick, G.M. / Escaja, N. / Alazzouzi, E. / Grandas, A. / Pedroso, E.
History
DepositionSep 11, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Jun 11, 1997Provider: 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_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'-CD(*P*AP*TP*TP*CP*AP*TP*TP*C)-3')
B: DNA (5'-CD(*P*AP*TP*TP*CP*AP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,28714
Polymers4,7532
Non-polymers1,53412
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)22.844, 27.676, 55.370
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'-CD(*P*AP*TP*TP*CP*AP*TP*TP*C)-3')


Mass: 2376.591 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ba
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 1.84 Å3/Da / Density % sol: 36 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA CACODYLATE11
3BA ACETATE11
4PEG 400011
5WATER12
6PEG 400012
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18.8 mMcacodylate1drop
213.2 mMbarium acetate1drop
314.7 %(w/v)PEG40001drop
430 %(w/v)PEG40001reservoir
51
61

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 18, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.1 Å / Num. obs: 19971 / % possible obs: 100 % / Rmerge(I) obs: 0.069
Reflection
*PLUS
Highest resolution: 1.1 Å / % possible obs: 100 % / Rmerge(I) obs: 0.067

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Processing

Software
NameClassification
SHELXL-96refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: HEAVY ATOM METHOD / Resolution: 1.1→9 Å / Num. parameters: 3484 / Num. restraintsaints: 4248 / σ(F): 4 / Stereochemistry target values: SHELXL
RfactorNum. reflection% reflection
obs0.199 12662 100 %
all-19924 -
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRanisotropic
ALL WATERSX-RAY DIFFRACTIONTRanisotropic
Refinement stepCycle: LAST / Resolution: 1.1→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 504 12 105 621
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.006
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 9 Å / σ(F): 4 / Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS

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